A fundamental study for the numerical scheme to simulate unsteady nonlinear waves by solving Euler equations is presented. First a conservation form and a non-conservation form of the Euler equations with a free surface fitted coordinate system are compared. Next, a time splitting fractional step method and an alternating direction implicit(ADI) method for the time integration are compared. For the comparative study, flow calculations around a bottom bump in a channel and a NACA 0012 hydrofoil in a flume are performed. The results show that the ADI method with a third order upwind differencing scheme is very efficient in reducing the computing time with keeping the accuracy, And, there is no distinct difference between two expression forms except that the non-conservative form shows faster wave propagating velocity than the conservation form. Some results are compared with experiments and show good agreement.