To improve the efficiency and flexibility of femtosecond laser fabrication, a holographic femtosecond laser parallel fabrication system was built. The relationship between the uniformity and the spatial distribution of multi-foci generated by Computer-generated Hologram (CGH) was studied. Firstly, a Spatial Light Modulator (SLM) was introduced into the femtosecond laser fabrication system. Then, Gerchberg-Saxton(GS) algorithm was used to design three foci arrays of straight-line distribution and triangular distribution. Finally, the effects of holograms designed by foci arrays of straight-line distribution and triangular distribution on the uniformity were compared by numerical simulation and experiments. The results show that the foci array of straight-line distribution is not easy to obtain higher uniformity, and its three-foci U is only by 79%; however, that of the triangular distribution tends to achieve higher uniformity and its three-foci U is about 100%. The experiment shows that the three foci of triangular distribution can implement a high quality parallel processing and obtained hemispheric microstructures have microlens array functions .