Effective manipulation on the state of the charge qubit system consisting of Josephson junctions by means of Lyapunov control theory is performed. Numerical simulations show that the manipulation on superconducting qubit system can be realized via choosing proper control amplitude whether directly or indirectly using the deviation based on Lyapunov method. Quantum system can be controlled by selecting the appropriate control range. The bigger the control amplitude is, the smoother the control function curve is, and the shorter the control task time is. This control method can avoid the interative calculation of complex traditional control methods, and ensure the stability of quantum system. Therefore Lyapunov method is a kind of practical manipulation method.