Fundamental understanding of liquid flow through microchannels with 3D prismatic elements is important to the design and operation of lab-on-a-chip devices. In this paper, we studied experimentally and theoretically the electroosmotic flow (EOF) in slit microchannels with rectangular 3D prismatic elements fabricated on the bottom channel wall. The average electroosmotic velocity measured by the current-monitoring technique was found lower than that in a smooth microchannel. This velocity reduction becomes larger in microchannel with larger but less number of the prisms even though the space taken by the prisms are identical. The velocity distribution and streamlines on two typical horizontal planes in the microchannel are measured and visualized by a particle-based technique. These experimental observations are in good agreement with the numerical simulation. The comparison of streamlines near the prisms in the pressure-driven flow with that in the EOF showed that the EOF was more sensitive to the local geometry.