The trend of capital flowing into rural areas has been a topic of debate, but its advantageous role in urban-rural integration cannot be overlooked. Understanding farmers’ preferences for cooperating with industrial capital provides essential theoretical support for effectively leveraging the linkage effect of commercial capital in rural development and promoting common prosperity. This study uses choice experiments and survey data from farmers in Funan, Anhui, and Liyang, Jiangsu, and analyzes the data using the AGIL model and the mixed Logit model. The findings reveal that farmers have a positive attitude toward cooperation with industrial capital. Specifically, regarding the supply side, farmers prefer “talented individuals returning home” > “outside enterprises”; for cooperation models, farmers’ preferences are ranked as “company + village collective + farmer” > “company + farmer” > “company + cooperative + farmer”; in terms of interest linkage mechanisms, farmers prefer “labor participation” > “market-driven” > “contractual agreement”. Contrary to expectations, farmers showed little variation in their preferences for service types. Based on these findings, the paper suggests that farmers’ principal role in cooperation models for capital investment projects in rural areas should be emphasized. It advocates for the development of multi-faceted interest linkage mechanisms and the encouragement of capable individuals who have moved away to return and invest locally. Moreover, enhancing the participatory capacity of village collective organizations is critical. Industrial and commercial capital should also actively integrate into rural social networks and contribute to the provision of public goods in rural areas.