In order to provide a method for evaluating flight control systems with the wind tunnel based virtual flight testing and provide a guide for building virtual flight testing systems, the virtual flight testing evaluation method was researched. The virtual flight testing evaluation method consisted of three parts: virtual flight testing method, virtual flight testing data processing method, and flight control system performance determination method, which were respectively designed for a pitching control system. Then, the hardware-in-the-loop simulation evaluation method was presented, and comparisons between the virtual flight testing and hardware-in-the-loop simulation evaluation method were conducted to highlight the characteristics of virtual flight testing evaluation method. Finally, virtual flight testing simulation models of a sample air vehicle were built and virtual flight testing were simulated to demonstrate the virtual flight testing evaluation method, which is helpful for the understanding of the virtual flight testing evaluation method with more sensibility. The evaluation results show that the virtual flight testing evaluation method designed can be used for flight control system evaluation.