Agriculture is the cornerstone of building a modern country. As the impact of global climate change on agricultural production intensifies, studying how agricultural enterprises can respond to challenges such as extreme weather and resource scarcity is crucial for improving agricultural adaptability and mitigating the negative effects of climate change. Based on empirical data of A-share agricultural listed companies from 2013 to 2022, fixed effect and mediation effect models were selected to test the impact of climate risk on business performance. The research results indicate that climate risk has a negative impact on the operational performance of agricultural enterprises, and green innovation plays a mediating role in it. Heterogeneity results show that non-state-owned enterprises are more significantly impacted by climate risk than state-owned enterprises. Important theoretical basis and practical guidance are provided for agricultural enterprises in addressing climate risks.