Vortex generator jets (VGJs) have been recognized as an effective active control method for the flow separation. To investigate its mechanism in conical diffuser, PIV was used to study the interaction of VGJs with freestream in this study. A conical diffuser model, with divergence angle of 14° was used. The jet holes were drilled with pitch angle of 30° and skew angle of 90°. At several streamwise locations, two-dimensional traverses were set up to obtain the velocity distribution and vorticity in the interaction region of vortex. PIV measurements provide a global depiction of the interaction of boundary layer transition and separation in this unsteady environment. It is shown that vortical flows generated by VGJs significantly fluctuate velocity profiles. The steady jets create vortices that swept the low momentum fluid up from the boundary layer while transporting high momentum freestream fluid towards the wall, which provides the ingredients for flow control. It is also revealed that the longitudinal vortices are generated in the boundary layer by shear stress and friction from jets, which increase cross-stream mixing of streamwise momentum and then suppress separation in conical diffuser. Some new phenomena and rules presented would offer valuable information for further study.