The reform of the homestead system is an important way to vacate inefficient and idle land, revitalize the stock, and visualize the asset properties of homesteads in the vast rural areas nowadays. In this study, we first carry out the selection of indicators for measuring the changes in farmers’ well-being under the reform of the homestead system and take a certain region that has carried out the reform of the rural land system as an example and use the fuzzy comprehensive evaluation to measure the changes in the overall well-being of the farmers in that region and the changes in the well-being of the farmers in different villages. The impact of the reform of the homestead system on farmers’ well-being is modeled using structural equations, and the corresponding hypotheses and validations are carried out. The analysis shows that farmers’ well-being in the study area improved by 0.254 overall and by 0.208, 0.204, and 0.350 in urban, peri-urban, and remote villages, respectively. The reform of the homestead system of uncompensated withdrawal, compensated withdrawal, compensated use, and construction of houses by farmers all positively affected the improvement of farmers’ well-being, with the compensated withdrawal policy having the greatest impact (0.315). It is necessary to innovate the homestead system, safeguard and expand farmers’ property rights, promote the reform of the expropriation system, and explore the establishment of a reasonable homestead withdrawal mechanism to encourage the further enhancement of farmers’ well-being.