In order to achieve rapid fabrication of hydrogel cell scaffolds, the computer-aided holographic method was employed into the traditional femtosecond laser two-photon processing. The generation of hologram as well as the influence of its parameters on the processed cylinder microstructure was studied. Firstly, Ring-shaped Bessel-beam holograms were generated according to the Bessel light wave equation and its transmission function, of which the parameters effect on the size and quality of ring structure was analyzed. Then the generated holograms were used to process tubes with a thickness of 0.8 μm and diameters from 8 μm to 15 μm in the polyethylene glycol double acrylate (PEGDA) hydrogel. Finally, an efficient and rapid processing of hydrogel cell scaffolds was realized experimentally and the diameter of hydrogel tubes was 8 μm. This technique can remarkably improve the efficiency of femtosecond laser processing, thus has great potential in many applications such as biological culture and chemical analyses.