Low power efficiency is a critical factor that restricts marketization development of the vertical axis wind turbine (VAWT). The proposal of the trailing edge flap can change flow structure on blade surface, so as to improve the aerodynamic performance of VAWT. At present, the variation law of aerodynamic performance of different airfoil VAWT with trailing edge flaps is not clear. Based on the computational fluid dynamics (CFD) method and the shear stress transport (SST) model, a numerical simulation of 3 H-type VAWTs with different airfoils (NACA0018, NACA0021, and NACA0024) with separated trailing edge flap is conducted. It is found that the results of the validation case are in good agreement with experimental results, which verifies the reliability of this method. Afterwards, 3 basic airfoils and 5 groups of flap deflection angle (-16°, -8°, 0°, 8°, and 16°) parameters are selected to explore the difference in the aerodynamic performance of VAWTs. The results indicate that the positive flap deflection angle in the upwind region can effectively improve blade moment coefficient, and the negative flap deflection angle in the downwind region has a beneficial effect. For the negative flap, the degree of wind energy utilization affected by deflection is positively correlated with airfoil thickness, while for the positive flap, the opposite is true. The research results of this paper can provide an effective reference for application of trailing edge flaps of vertical axis wind turbines.