The aerodynamic performance of the variable cycle engine fan changes sharply during mode transition. Investigating the variations of flow structure and understanding the loss mechanism are helpful in providing guidance for the fan design. Three-dimensional models of single bypass and double bypass compression systems are established, and static pressure is applied at the bypass stream outlet to simulate the opening of the mode selection valve. The characteristic band of variable cycle engine fan is obtained by gradually increasing the bypass stream pressure while maintaining specific values for the core stream pressure. Results show that the overall performance of the double bypass configuration, without bypass recirculation, is almost identical to that of the conventional single bypass configuration during the throttling process. With the increase in bypass pressure, the shock wave and the trajectory of tip leakage vortex gradually move forward, thereby increasing the blockage region induced by the interaction between the shock and tip leakage vortex. In addition, the performance of fan with reverse flow is also calculated. The recirculation causes the operating point to move closer to the stability limit, reducing the isentropic efficiency. Additionally, the recirculation changes the radial distribution of axial velocity and total pressure, leading to inlet distortion in the core driven fan stage. Furthermore, the loss mechanism is clarified by modeling the splitter and conducting entropy generation analysis. The sharp expansion of bypass stream could cause severe flow separation, and reducing the curvature of casing can effectively suppress the viscous shear loss.