Vortex generators (VGs) are applied to a two-stage highly-loaded transonic fan using the full blended blade and endwall (F-BBEW) method to assess their effects on fan performance. In the last stage stator, VGs were arranged on the hub and shroud within the blade passages. Numerical simulations are conducted to explore the effects of VGs on performance of the highly loaded transonic fan and the VGs action mechanism. The results demonstrate that the implementation of VGs led to an increase in fan aerodynamic performance, improving the fan pressure ratio margin by 2.25% while maintaining efficiency. The total pressure loss of the last stage stator decreased, with the loss coefficient reduced from 5.33% to 4.58% at 1.15 times the design pressure ratio. Furthermore, the VGs improve the flow field of the last stage stator. While the VGs on the hub suppressed local secondary flows, they do not provide significant benefits due to interaction with shock waves. In contrast, the VGs on the shroud reduce secondary flows and mitigate separation induced by upstream VGs, improving corner flow and overall flow quality of the last stage stator.