[Objective] Large language models (LLMs) have demonstrated strong capabilities in natural language understanding, knowledge integration, and complex reasoning, offering new opportunities for intelligent decision-making in agriculture. However, their direct application in agricultural production and facility environment control remains challenging due to strong physical constraints and high operational risks. The lack of real-world interaction and executable decision grounding limits the practical effectiveness of conventional LLMs in such scenarios. To address these challenges, a tool-augmented LLM-based agricultural intelligent agent system, termed AgriAgent, was proposed, and a digital-twin-based evaluation platform for agricultural decision-making was developed. By integrating a high-fidelity digital twin environment with an end-to-end agent architecture, the decision-making performance of agricultural intelligent agents with different parameter scales was systematically evaluated across multiple crops and climate scenarios. [Methods] A high-fidelity agricultural digital twin evaluation platform was constructed using the decision support system for agrotechnology transfer (DSSAT) v4.8 crop growth model as the core simulation engine to model crop growth under diverse environmental conditions and management strategies. Meteorological driving data were obtained from the Seoul Historical Weather Data dataset. Through data cleaning, missing-value imputation, unit normalization, and time-series reconstruction, the raw meteorological data were transformed into standardized inputs compatible with DSSAT. Three climate scenarios representing different environmental complexities were designed, including a regular scenario, a perturbed scenario, and an extreme scenario. The regular scenario employed historical observations, the perturbed scenario introduced stochastic disturbances to simulate short-term climate variability, and the extreme scenario incorporated multi-factor coupled stresses such as high temperatures and excessive precipitation during sensitive growth stages. In total, 90 annual climate driving sequences were generated. Fixed soil profile parameters calibrated by domain experts were applied across all simulations to minimize confounding effects. Within this digital twin environment, a tool-augmented agricultural intelligent agent, AgriAgent, was implemented using a modular architecture consisting of a sensor module, memory module, retriever, large language model, and tool executor, forming a closed-loop decision-making framework. In each decision cycle, the agent perceived environmental and crop state information, including soil moisture and nutrient status, meteorological conditions, crop growth stages, and stress indicators. State summaries and historical decisions were stored in memory, while agronomic knowledge was retrieved through a retrieval-augmented generation mechanism. Based on integrated information, the LLM generated structured environmental control commands in JSON format, which were validated and constrained by the tool executor before updating the DSSAT environment. The system supported irrigation, supplementary lighting, ventilation, heating, fertilization, and CO₂ enrichment. Five representative crops: maize, millet, sugar beet, tomato, and cabbage were simulated under the three climate scenarios over complete growing seasons, resulting in 450 crop-scenario combinations. An unmanaged DSSAT simulation served as the baseline. AgriAgent models with three parameter scales (1.5B, 3B, and 7B), built on the Qwen2.5 series, were evaluated. Crop economic yield expressed as dry matter at physiological maturity was adopted as the evaluation metric. [Results and Discussions] The results showed that AgriAgent consistently outperformed the baseline across all crops and climate scenarios, with model scale exerting a significant influence on decision-making performance. AgriAgent-7B achieved the best overall performance under regular, perturbed, and extreme scenarios, demonstrating strong generalization ability and environmental adaptability. By dynamically adjusting water, nutrient, light, and thermal management strategies, the agent effectively mitigated environmental stresses even under multi-factor coupled extreme climate conditions. Under extreme scenarios, AgriAgent-7B increased yields by 463.60% for maize, 351.20% for millet, 125.40% for sugar beet, 1 537.46% for tomato, and 1 185.14% for cabbage compared with the baseline. Particularly large gains were observed for high-value crops such as tomato and cabbage, highlighting the advantages of the proposed framework for precision-controlled facility agriculture. In contrast, AgriAgent-1.5B exhibited performance comparable to the baseline, while AgriAgent-3B achieved moderate improvements but remained inferior to the 7B model. These findings indicate a clear scaling effect, suggesting that larger models possess stronger capabilities in multi-source information integration, long-term temporal reasoning, and adaptation to complex environments. [Conclusions] This study developed a digital-twin-based agricultural decision evaluation platform and proposed a tool-augmented, end-to-end agricultural intelligent agent named AgriAgent. Experiments across multiple crops and climate scenarios verified the effectiveness and robustness of the proposed framework for dynamic agricultural decision-making. The results demonstrate that integrating knowledge retrieval, reasoning, and tool execution within a closed-loop LLM-based agent enables stable, reliable, and adaptive environmental control, providing a feasible technical pathway and standardized evaluation paradigm for intelligent agriculture.