The authors developed a debris flow simulator by Finite Element Method which could properly computes the process of erosion and sediment around slit type Sabo dam. In the simulator, shallow water wave equation describes debris flow and stabilized FEM is used as a method of discretization. There are two ways to define unknown in continuous equation of shallow water wave. One, the difference between reference surface and water surface is set as unknown (Way I), and the other is water depth itself as unknown (Way II). When simulator is applied to Way II, it might produce unreasonable high water depth in the discontinuous zone such as dams. This is because the diffusion effect of shock capturing term distributes water depth to the neighbor nodes counter to irregular water surface. In order to resolve this problem, the authors propose an alternative definition of reference surface used in Way I. The new definition keeps the surface evenly in the discontinuous zone which produces uneven surface in usual manner. Proposed reference surface reduces unrealistic high water depth in the discontinuous zone and stabilizes calculation process. A hydraulic experiment with slit-type Sabo dam miniature was used to verify the proposed method and qualitatively consistent result was showed. In addition, a full-scale grid type Sabo dam was simulated and comparison was made between the varying slit widths. With one more study cases, changes of flow around Sabo dams and of riverbed were calculated adequately, the validity and effectiveness of the debris flow simulator by FEM are proved in this paper.