The construction of the natural protected area (NPA) system is a fundamental component of China's ecological civilization initiative, yet the spatial alignment between existing NPAs and regional key ecological spaces remains poorly defined, leading to exacerbated habitat isolation and landscape fragmentation. This study focuses on the Fuchun River Basin, a region covering 3,829.15 km² and spanning nine districts - including Yuhang, Xiaoshan, and Fuyang - characterized by significant ecological value and rapid urbanization. Facing the challenges of increasingly fragmented ecological land and intense human-land contradictions, this research aims to identify protection gaps and optimize the spatial configuration of NPAs by constructing a comprehensive regional ecological network. The study integrates diverse quantitative methods to ensure scientific rigor: the InVEST model was first employed to evaluate four key ecosystem services, specifically water yield, soil conservation, carbon sequestration, and habitat quality. Simultaneously, cultural services were quantified through a Python-based accessibility analysis of recreation points using Gaode Map API data to account for the "intangible" value of the landscape. Morphological Spatial Pattern Analysis (MSPA) was subsequently applied to identify core landscape patches, and 25 ecological sources totaling 557.39 km² (representing 14.56% of the basin) were selected based on a patch importance index (dPC) threshold of greater than 0.5. To develop a scientific resistance surface, Spatial Principal Component Analysis (SPCA) was utilized to determine the weights of seven resistance factors - including elevation, slope, land cover, NDVI, and proximity to railways and roads - effectively eliminating data redundancy and avoiding the subjectivity of manual weighting. Utilizing circuit theory and the linkage mapper tool, the study extracted 54 ecological corridors with a total length of 684.55 km and a combined area of 632.80 km². Furthermore, the research identified 114 critical ecological pinch points covering 8.61 km², which represent high-current density areas indispensable for maintaining regional connectivity and species flow. Spatial overlay analysis revealed significant mismatches between current conservation efforts and ecological needs: within the 650.56 km² of existing NPAs, only 173.86 km² (26.89%) overlapped with identified ecological sources, and 114.60 km² (17.62%) coincided with ecological corridors. Notably, ten key ecological sources were found to be entirely independent of the current NPA system, highlighting major protection gaps. Based on these findings, a three-tier spatial optimization framework is proposed: first, the designation of Strict Protection Zones (280 km²) at the intersection of the ecological network and existing NPAs, where human interference is strictly prohibited and buffer zones are established to maintain stable natural succession; second, the identification of Ecological Restoration Zones (370 km²) in areas where ecosystem services are degraded, requiring near-natural restoration, agricultural remediation, and restricted development; and third, the delimitation of Potential Protection Zones (386.73 km²) to incorporate high-value sources and pinch points currently lacking protection by merging adjacent areas or establishing "stepping stones" for migrating species. This study adopts a systemic ecological network perspective to provide scientific evidence and categorized management suggestions for NPA integration under the "One Map" territorial planning framework, offering profound practical guidance for enhancing regional ecological stability.