Compared with polymer-based biochips, such as polydimethylsiloxane (PDMS), glass based chips have drawn much attention due to their high transparency, chemical stability, and good biocompatibility. This paper investigated the glass molding process (GMP) for fabricating microstructures of microfluidic chips. The glass material was D-ZK3. Firstly, a mold with protrusion microstructure was prepared and used to fabricate grooves to evaluate the GMP performance in terms of roughness and height. Next, the molds for fabricating three typical microfluidic chips, for example, diffusion mixer chip, flow focusing chip, and cell counting chip, were prepared and used to mold microfluidic chips. The analysis of mold wear was then conducted by the comparison of mold morphology, before and after the GMP, which indicated that the mold was suitable for GMP. Finally, in order to verify the performance of the molded chips by the GMP, a mixed microfluidic chip was chosen to conduct an actual liquid filling experiment. The study indicated that the fabricating microstructure of glass microfluidic chip could be finished in 12 min with good surface quality, thus, providing a promising method for achieving mass production of glass microfluidic chips in the future.