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Based on the dual context of accelerating comprehensive green transformation of the economy and society and modernizing government governance during the 15th Five-Year Plan period, this study utilizes panel data from 280 prefecture-level cities in China from 2006 to 2023 to systematically examine the impact of public sector personnel size on green total factor productivity (GTFP) and its underlying mechanisms. The study employs a non-radial, non-directional SBM-DDF model to measure GTFP across cities and conducts empirical tests using fixed effects models, mediation effect models, and spatial Durbin models. Results reveal that public sector personnel size exerts a linear inhibitory effect on GTFP, with an inverted "U"-shaped relationship between personnel size and technical efficiency (EC). Heterogeneity analysis indicates that this inhibitory effect is particularly pronounced in central and western regions as well as cities with moderate economic development levels. Spatial effect tests demonstrate that, constrained by administrative boundaries and institutional environments, the impact of public sector personnel size on GTFP exhibits significant local effects without spatial spillover effects. Mechanism tests further reveal that expansion of public sector personnel size distorts regional population mobility patterns through the "institutional internal siphon effect," and indirectly inhibits GTFP growth by crowding out R&D investment and suppressing production organization transformation, thereby hindering the enhancement of new-quality productivity. This study provides crucial micro-level evidence and policy insights for dynamically optimizing government staffing structures during the 15th Five-Year Plan period, mitigating the crowding-out effects of fiscal support scale expansion on green innovation, and achieving efficient green governance.