Abstract: To meet the demand for hydrogel microcapsule fabrication, this study aimed to develop a high-throughput system based on a 3D microfluidic chip for producing core-shell microcapsules. The system uses 3D micro-/nano printing technology, which offers fast prototyping, low cost, and high precision. This method allows precise control over the structure of the microcapsules. The system includes a droplet microfluidic chip with 3D microstructures. These are made using a dual-layer sheath flow strategy to generate the microcapsules. Experimental results show that the flow-focusing region on the inner bottom surface of the 3D micro/nano-printed mold has a flatness of 4.65 μm. The dimensional errors in the three-phase channels are always less than 2 μm. Similarly, the PDMS plate that holds the microchannels shows a flatness of 4.81 μm. The channel dimensional errors in the PDMS plate are also within 2 μm. These results indicate that both the mold and the PDMS plate have high flatness and accuracy. They meet the technical requirements for making microcapsules. Microcapsules with different inner diameters were created by changing the flow rate of the core solution (120, 100, 80, 60, and 40 μL/h). The outer diameter stayed nearly the same. The microcapsules made by the system have a very low coefficient of variation (CV) for both outer and inner diameters (<3%), showing that the capsules are very uniform in size. Finally, cell culture tests were done to check the biocompatibility and function of the microcapsules. A549 cells showed clear growth and clustering after two days of culture inside the microcapsules. This proves that the microcapsules from this system support cell growth well. These results suggest that the system has great potential for large-scale use in biomedical fields.