We present a study on Taylor vortex flow in between a rotating inner cylinder and a stationary outer cylinder with vertical or horizontal baffles. A mineral oil is used as the working fluid in the annular channel of 60 mm in height and 11.6 mm in gap width. The flow pattern in the annulus is investigated by particle image velocimetry (PIV) and computational fluid dynamics (CFD). Both the experimental and simulation results show that the presence of vertical baffles influences the vertical positions of vortices—it is primarily significant for the bottom vortex. Increasing number of vertical baffles gradually decreases the azimuthal variation in the vertical position. The baffles also lead to the occurrence of a circulation flow immediately upstream and downstream each baffle plate in the radial–azimuthal plane. On the other hand, an annular horizontal baffle with sufficient width alters the vortex structure in the gap, for instance, fewer vortices are observed. With two horizontal baffles in the annulus, the flow pattern is largely affected by the baffle width and the distance between the two baffles. This study provides a better understanding of Taylor vortex in presence of internal baffles, which will be important for practical applications of Taylor vortex devices.