This paper discusses the applicability of a MacCormack finite difference scheme in a generalized coordinate system to flood flows in simplified basin models located in mountainous areas. The calculated results show that among three kinds of combinations of 1-D operators in the MacCormack finite difference scheme employing direction splitting method, the scheme with alternating difference directions is the best to eliminate truncation errors resulting from the fixed direction difference scheme. This scheme can produce almost similar results for different grid systems and can use small artificial viscosity to simulate experimental results stably. The scheme proves to predict well flood flow characteristics in basins with an incised channel or a tributary.