Rainstorms easily can cause serious secondary disasters such as waterlogging, debris flow, and flood, and the combination of these secondary disasters makes cities more vulnerable. However, to date, few studies have considered the joint effects of rainstorm secondary disasters, and the common procedures or methods for joint risk assessment have not been developed. Considering the joint effects of rainstorm waterlogging and rainstorm debris flow, this paper proposes a modeling method for joint risk assessment based on multisource spatial data including meteorological data, geological data, and building data, and analyzed the residential buildings in a built-up area of Wuhan East Lake High-Tech Development Zone, China. First, the improved rainstorm waterlogging model was proposed to generate waterlogging simulation results with consideration of the influences of rain storage facilities such as lakes and reservoirs on waterlogging results. Second, the rainstorm debris flow model was employed to generate the simulation results of debris flow. Then the damage to residences were calculated with stage-damage curves under single secondary disasters. Finally, a Bayesian network model was built and applied to generate the joint risk of the secondary disasters according to the simulation results of waterlogging and debris flow. The results show that the joint effects of waterlogging and debris flow first increase and then decrease with the increase of precipitation. The joint disaster loss cannot simply be calculated by finding the maximum or sum of the single disaster losses, but must be obtained with a specific reasoning method. The joint disaster loss presented evident spatial disparities. The secondary disasters mainly affected the area near northern mountains, the central area was in the medium-risk zone, and the other areas were less affected. The annual average loss of residential buildings in the studied area was CNY 15.82 million. The findings provide important information for the local area and are expected to help the rainstorm risk management of other jurisdictions.