Virtual vortex gear is a sequentially introduced vortex flow on a microfluidic chip. The directions of every two closed-by vortices are opposite to each other, which is similar to a set of gears, and thus, is named 'virtual vortex gear'. In this work, we proposed an experimental method to investigate the 3D flow patterns of the vortices. By adjusting the focal plane of the objective lens in a microscope, we can directly observe the flow of the vortices at different layers. We found the flow-pattern are very different from layer to layer, and spiral flows across layers were observed inside the vortex. Computational simulations were performed for comparison, and the results well match to the experimental results. A possible flow mechanism is proposed based on the analysis. Finally, virtual vortex gear has been tested with red blood cells for the feasibility of mixing particles with celllevel size.