Plateau lake regions face escalating conflicts between food production and ecosystem conservation under rapid urbanization and strict ecological regulation. However, existing evaluations often overlook the positive ecosystem services generated by cultivated land and fail to capture the nonlinear mechanisms shaping eco-efficiency of cultivated land use (ECLU). This study develops an ecosystem service-based framework to assess the ECLU of Kunming, a typical plateau lake-basin city in southwest China, from 2005 to 2022. Ecosystem service value (ESV) is incorporated as a desirable output within a super-efficiency SBM model, and an XGBoost–SHAP approach is applied to identify the intensity, nonlinear thresholds and interaction mechanisms. Results show an average ECLU of 1.12 with a fluctuating downward trend and widening spatial disparities. High-efficiency zones cluster in central–southern regions, while urbanizing cores experience ecological function degradation despite productivity gains. Cultivated land fragmentation is the dominant barrier, with a critical threshold of 31.90 mu, and fertilizer intensity turns detrimental beyond 0.19 t/ha. Urbanization exhibits an inverted-U pattern—initially suppressive (55%)—with the promotion phase weakened by approximately 67% under severe fragmentation. Globally, threshold-based zoning and fragmentation mitigation must precede fertilizer optimization to ensure synergistic benefits.

Yunnan Province, which is located in the mountainous plateau region of China, faces numerous challenges, including the population decline of rural areas. Achieving coordinated development between the transportation and rural population systems is crucial for fostering sustainable growth. In this study, we developed a rural population pressure state response (PPSR) model and a comprehensive transport superiority (TS) model that considers the influence of aviation. We quantified the rural population system and horizontal transportation superiority across Yunnan’s districts and counties for the period 2013 to 2021, examining their temporal and spatial heterogeneity. Using a spatial autocorrelation model, we also explored the trade-offs and synergy between Yunnan’s TS and PPSR. The main findings are as follows. (1) From 2013 to 2021, the spatial polarization pattern of PPSR in Yunnan Province gradually weakened, and there were different degrees of rural contraction overall. (2) From 2013 to 2021, Yunnan’s TS significantly increased, with aviation conditions having a notably positive impact, further strengthening Kunming’s position as the regional core. (3) In Yunnan, the relationship between TS and PPSR is significant, with a collaborative pattern emerging across districts and counties, reflecting distinct regional characteristics and a degree of polarization. This study provides valuable insights for integrating urban and rural development in plateau and mountainous areas and offers a new perspective for rural revitalization.