Guiding farmers to voluntarily exit idle homesteads is an effective way to improve the quality of homestead management, and the integrated development of urban-rural areas provides a driving force for the exit. Based on the theoretical framework of urban-rural integration and intergenerational effects, and applying survey data of Jianou city, Fujian, this study analyzed the willingness to exit from idle homestead, and explores the influence mechanism of the urbanization and farmers’ intergeneration on the homestead exit willingness by the Probit, the IV-Probit and the moderation models. Results show that farmers are more willing to exit homesteads, and 65.77% of farmers are willing to exchange the idle homesteads for a payment, and pursuit of better work conditions and public services in the city is the main incentive for them to give up their homesteads. The level of population and economic integration has a significant impact on farmers’ willingness to exit their homesteads, while the land and social integration have a negative impact. The heterogeneity analysis indicates that suburban farmers’ willingness is significantly influenced by the population integration. Generation can regulate the influence direction of urban-rural integration, the population and economic integration positively improve the willingness of newer generation to quit homesteads, and the land and social integration levels inhibit the exit willingness of the older generation. To promote homestead exit, this paper puts forward some countermeasures and suggestions, including coordinately managing the urban housing permit and rural homestead permit to prioritize homestead management system, promoting the transformation of homestead reform achievement to development dividend and governance effectiveness, and improving farmers’ integration ability.