<p>China, accounting for approximately one-quarter of global grain production, faces increasing pressure to balance agricultural productivity with environmental sustainability. While conventional agricultural total factor productivity (ATFP) measures economic performance, this study develops an enhanced agricultural ecological total factor productivity (AETFP) index that incorporates ecosystem service values (ESV) to simultaneously evaluate economic and ecological dimensions. Using a three-stage slack-based DEA approach that controls for external environmental factors and statistical noise, regional productivity across China during 2009–2023 is quantified. The findings reveal several important patterns. The western region demonstrates relatively high ESV levels, though these remain below the national optimum, whereas the eastern region maintains a leading position in both ATFP and AETFP. At the provincial level, the comparison between AETFP and ATFP highlights clear ecological–economic efficiency trade-offs. Furthermore, a multi-scale analysis of city clusters indicates that the spatial spillover effects of AETFP are considerably weaker than those of economic productivity, reflecting the spatial specificity of ecosystem services and the role of institutional constraints. Finally, policy interventions such as ecological subsidies and financial support exhibit geographically heterogeneous effects, with the most balanced improvements observed in provinces facing moderate external conditions. Targeted policy recommendations are proposed to achieve sustainable agricultural intensification.</p>