Research purpose: to analyze farmers’ willingness to gather homestead and its influencing factors, so as to provide decision-making basis for the rational layout of rural homestead. Methods: questionnaire, logistic model. The results are as follows. (1) Farmers’ willingness to gather homesteads is highest in dam areas, followed by hilly areas, and is lowest in mountainous areas. (2) The respondents’ age, family support ratio, housing structure, whether the access road is paved, and the distance from the main road have significant negative impacts on farmers’ willingness to gather homesteads, while homesteads being idle, the service life of the house, the type of daily energy use, and whether they are far from relatives after relocation have significant positive impacts on farmers’ willingness to gather homesteads. (3) The main influencing factors of farmers’ homestead agglomeration in dam areas are the idle situation of a homestead, housing structure, the service life of the house, and whether they are satisfied with their current homestead residence. (4) The main influencing factors of farmers’ homestead agglomeration in hilly areas are the age of the respondents, the proportion of family workers, and whether they accept the relocation and are far from relatives. (5) The main influencing factors of farmers’ homestead agglomeration in mountainous areas are the age of the respondents, the ratio of family support, the housing structure, and whether the access road is paved. We conclude that there are significant differences in farmers’ willingness to gather homesteads and the influencing factors in different geomorphic areas. Policy makers should formulate differentiated homestead agglomeration optimization schemes and design the optimization paths of homestead agglomeration on the basis of geomorphic classification and subregion.