With the advancement of agricultural modernization, farmer cooperatives play a vital role in enhancing agricultural production efficiency and improving farmers" income. However, they continue to face challenges such as capital shortages and insufficient technological support. As a key policy tool to promote the high-quality development of farmer cooperatives, government subsidies have attracted considerable attention from both academia and policymakers—particularly regarding their effectiveness and the mediating role of scale expansion. Based on survey data from 229 farmer cooperatives in Heilongjiang and Anhui provinces, this study constructs an evaluation framework for the high-quality development of farmer cooperatives across four dimensions: standardization level, operational level, service capacity, and driving capacity. Using the Ordinary Least Squares (OLS) method, the study examines the direct impact of government subsidies on the high-quality development of farmer cooperatives and employs a mediating effect model to test the role of scale expansion in this relationship. The findings indicate that government subsidies have a significant positive effect on the high-quality development of farmer cooperatives. Among the four dimensions, the most substantial improvement is observed in service capacity, followed by standardization level, while the effects on driving capacity and operational level are comparatively modest. Moreover, scale expansion exhibits a significant and positive mediating effect, suggesting that government subsidies indirectly promote cooperative development by facilitating scale expansion. Additionally, the study uncovers heterogeneous effects across cooperatives at different developmental stages. Start-up cooperatives are most responsive to government subsidies, while mature cooperatives show more stable but less pronounced effects. Based on these findings, this paper proposes several policy recommendations: enhancing the precision of subsidy policies, improving supporting measures for scale expansion, designing differentiated subsidy schemes tailored to cooperative characteristics, and strengthening the supervision of subsidy utilization. These recommendations aim to optimize the effectiveness of government subsidies and provide strong support for the high-quality development of farmer cooperatives.