In recent years, the increasing penetration level of wind energy into power systems has brought new issues and challenges. One of the main concerns is the issue of dynamic response capability during outer disturbance conditions, especially the fault-tolerance capability during asymmetrical faults. In order to improve the fault-tolerance and dynamic response capability under asymmetrical grid fault conditions, an optimal integrated control scheme for the grid-side voltage-source converter (VSC) of direct-driven permanent magnet synchronous generator (PMSG)-based wind turbine systems is proposed in this paper. The optimal control strategy includes a main controller and an additional controller. In the main controller, a double-loop controller based on differential flatness-based theory is designed for grid-side VSC. Two parts are involved in the design process of the flatness-based controller: the reference trajectories generation of flatness output and the implementation of the controller. In the additional control aspect, an auxiliary second harmonic compensation control loop based on an improved calculation method for grid-side instantaneous transmission power is designed by the quasi proportional resonant (Quasi-PR) control principle, which is able to simultaneously restrain the second harmonic components in active power and reactive power injected into the grid without the respective calculation for current control references. Moreover, to reduce the DC-link overvoltage during grid faults, the mathematical model of DC-link voltage is analyzed and a feedforward modified control factor is added to the traditional DC voltage control loop in grid-side VSC. The effectiveness of the optimal control scheme is verified in PSCAD/EMTDC simulation software.