Abstract: The authors have proved that the Box method is unstable in three dimensional boundary layer calculation although it is stable in two dimensional boundary layer calculations.The Neumman stability analysis method has been applied to dealing with this problem.But the stablity equation obtained is too complex to solve analytically,so the numerical computations have been proposed,and some valuable conclusions have been drawn.The results are in accordance with the phenomena that occured in three dimensional boundary layer calculations with Box method.