In this paper, a new scheme is presented for the accurate tracking control of the second-order variable structure systems using the variable boundary layer. Up to now, variable structure controller(VSC) applying the variable boundary layer did not remove chattering from an arbitrary initial state of the system trajectory because VSC has used the fixed sliding surface. But, by using the linear time-varying sliding surfaces, the scheme has the robustness against chattering from all states. The suggested method can be applied to the second-order nonlinear systems with parameter uncertainty and extraneous disturbances, and have better tracking performance than the conventional method.To demonstrate the advantages of the proposed algorithm, it is applied to a two-link manipulator.