With the rapid promotion of urbanization and the implementation of the three-rights separation policy of rural homesteads, the withdrawal of rural homesteads has become a general trend. Withdrawal of rural homestead is an important path to implement the rural revitalization strategy and promote the integrated development of urban and rural areas. Therefore, the research on the risk of withdrawal of homestead is a necessary step to do a good job of withdrawal of rural homestead. Based on a micro perspective, we evaluate the risk of rural homestead withdrawal in the second round of pilot homestead reform counties and cities in Jilin Province based on four aspects: household economy, land withdrawal decision, social security and housing conditions. By constructing a risk evaluation index system after the withdrawal of the rural homestead, the risk matrix method was applied to evaluating and analyzing the risk factors of the withdrawal of the rural homestead. First, the results show that the withdrawal of rural homestead will touch farmers' rights and micro-welfare boundaries to a certain extent, which will lead to the risk of rural homestead withdrawal. Second, the results show that the overall risk level of rural homestead withdrawal in Jiutai District and Tongyu County of Jilin Province is not high, with most of the 12 risk indicators being medium to low risk, with compensation for homestead withdrawal, policy interpretation, medical services, children's education, and housing status being medium risk indicators, and agricultural income, participation in decision-making, accessibility, and community relations being low risk indicators. Third, the results show that the risk of daily household consumption, per capita household income and employment opportunities are high alert risks, which should be paid attention to, with a focus on solving economic problems and improving the rural homestead withdrawal mechanism to dovetail with social security to reduce the impact of these risks. Therefore, this article puts forward the following five targeted risk prevention suggestions in order to avoid and reduce the risk of rural homestead withdrawal. First, the homestead rural withdrawal process should clarify the homestead withdrawal policy and highlight the main position of farmers. Second, the process of rural homestead withdrawal should be innovative in the form of rural homestead withdrawal and reasonably determine the compensation standard. Third, the social security system should be improved and the employment training system of farmers, and it should be improved to ensure that the living standard of farmers will not decline and their long-term livelihood will be guaranteed. Fourth, the implementation of rural homestead withdrawal and resettlement according to different types of location can be convenient to ensure the comfort and satisfaction of farmers moving out. Fifth, a mechanism to supervise the risk of rural homestead withdrawal should be established and the risk of rural homestead withdrawal should be effectively prevented.