Linkages between rural migration and agricultural restructuring have become a key aspect of rapid urbanization in developing countries and a research focus for optimizing rural–urban development and rural reconstruction. Using continuous statistical data from the mountains of Southwest China, we examined the structure, changes and regional differences in agricultural cultivation under urbanization, analyzed the reasons for the restructuring of agricultural cultivation, and revealed the adaptation linkages between the rural–urban transition and agricultural restructuring. The results showed that land-use changes and rural migration caused by urbanization significantly affected the cultivation structure and its change trends: the proportion of food crops decreased, while the proportion of vegetables and orchards increased. However, regional differences in the agricultural cultivation structure were significant in the various township zones. Rural migration weakened agricultural cultivation in the lake basin and nationality townships but enhanced agricultural cultivation in the river valley townships. On the basis of the adaptation linkages of urbanization, rural migration, agricultural intensification, cultivation structure and economic development, chain-type changes and adaptation processes between rural migration and agricultural restructuring were demonstrated. These findings indicate that favorable locations and appropriate policies can promote the integration and restructuring of smallholder agriculture for commercialization and intensification and vice versa.