In order to reduce the loss caused by the secondary flow in the end wall area of the blade root of the micro-axial flow fan, according to the flow control idea of the vortex generator, a new type of flow control method was proposed. In this method, a micro straight plate was set on the pressure surface side of the leading edge of the blade root. Taking a micro-axial fan as the research object, the effects of vortex generators with different installation angles on the aerodynamic performance of the axial fan and internal flow field were analyzed by numerical simulation combined with experiments. The research results showed that the vortex generator had the best geometric installation angle to improve the static pressure and static pressure efficiency of the fan. The vortex generator affected the internal flow field of the impeller. Mixing of the induced vortex formed by the vortex generator with the pressure-side horseshoe vortex branch would weaken the strength of the horseshoe vortex, inhibiting to a certain extent the development of the channel vortex evolved by the participation of the horseshoe vortex, allowing redistribution of the fluid in the impeller flow path. In the macroscopic aspect, the vortex generator with matching structure can improve the aerodynamic performance of the fan. When the installation angle of the vortex generator was 15°, compared with the prototype fan in the high-efficiency operation range of the fan, the static pressure of the fan with the vortex generator was increased by up to 8%, and the static pressure efficiency was increased by up to 2.4%. For micro-axial fans with a large wheel-to-hub ratio, the secondary flow loss caused by channel vortices cannot be ignored. At the same time, attention should be paid to the structural design at the end wall of blade root in the optimization of impeller design.