There are few numerical models on rainfall runoff in hills-plain-wetland compound area, and the existing models can not definitely reflect the characteristics of hydrological elements spatial distribution and hydrological cycle in wetland. A numerical model on rainfall runoff was constructed in hills-plain-wetland compound area by using lattice Boltzmann method (LBM) and finite element method. When constructing the model, the compound area was divided into upstream hilly region with great topographic relief and downstream plain wetland with little topographic relief. In the upstream hilly region, spatial distribution of rainfall was calculated with the inverse distance method, soil motion model in unsaturated zone was constructed with LBM, water flow model in saturated zone was constructed with Darcy formula, numerical model of runoff was constructed with LBM, and then the numerical model of upstream rainfall runoff was constructed. Numerical model of water flow on plain wetland was constructed by using the finite element method with quadrilateral element. The entry water level boundary of plain wetland used the numerical output water level process of rainfall runoff in upper reaches, and export water level in plain wetland was achieved by calculating the export water process of watershed based on the numerical model constructed with LBM. The flow motion equation was solved with quadrilateral finite element method, which realized the seamless connection of the upstream area and the downstream area, and made the application of the model more convenient. Rainfall runoff and flow in plain area was simulated, with the Naoli river watershed as an example, and the simulation result was good, which means that the model is reliable.