China’s rural population has declined markedly with the acceleration of urbanization and industrialization, but the area under rural homesteads has continued to expand. Proper rural land use and management require large-scale, efficient, and low-cost rural residential surveys; however, such surveys are time-consuming and difficult to accomplish. Unmanned aerial vehicle (UAV) technology coupled with a deep learning architecture and 3D modelling can provide a potential alternative to traditional surveys for gathering rural homestead information. In this study, a method to estimate the village-level homestead area, a 3D-based building height model (BHM), and the number of building floors based on UAV imagery and the U-net algorithm was developed, and the respective estimation accuracies were found to be 0.92, 0.99, and 0.89. This method is rapid and inexpensive compared to the traditional time-consuming and costly household surveys, and, thus, it is of great significance to the ongoing use and management of rural homestead information, especially with regards to the confirmation of homestead property rights in China. Further, the proposed combination of UAV imagery and U-net technology may have a broader application in rural household surveys, as it can provide more information for decision-makers to grasp the current state of the rural socio-economic environment.