In this paper,we study a numerical solution of diffusion equation.We propose a three level-nine-point implicit difference scheme and prove the difference scheme is compatible with diffusion equation,second order convergent,unconditionally stable.A numerical experiments show,the difference scheme works well inside domain,but not near the discontinuous initial-boundary points,there are still has a vibration even though it was proved unconditionally stable theoretically.We take an action to solve the disturbance,give an Algorithm,Algorithm says,we must do some primal work at the discontinuous-initial-boundary points,then starting numerical solution according the three level-nine-point implicit difference scheme we proposed in this paper.The numerical example is done once again,and there is no disturbance or vibration,our Algorithm performed well all in domain and on the boundary points with small error and good accuracy,so the Algorithm we recommended is feasible and effective.