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.