Protein nanocapsules have been demonstrated to be an intracellular protein platform for protein drug delivery. However, traditional production techniques of nanocapsules are not quite suitable for obtaining high protein load efficiency and uniformity of the nanocapsules because of their existing difficulties in homogeneously mixing nanocapsule precursors and heat transfer. Herein, we report a simple way to produce protein nanocapsules using a low cost, easy-to-use millifluidic device that we designed to improve the protein load efficiency as well as the uniformity of the nanocapsules while maintaining the bioactivity of their inner protein and good biocompatibility. The synthesized nanocapsules were carefully characterized and the biocompatibility of these nanocapsules was verified. Besides, acute toxicity test, blood compatibility assay and vascular stimulation test were performed to prepare for clinical applications in the future. The results showed that the nanocapsules synthesized by the device were about 18 nm in size and had a higher protein load efficiency as well as a narrower size distribution (PDI: 0.343) than those of the nanocapsules synthesized by the commonly used bulk mixing method. Moreover, these nanocapsules can well ensure the functions of their inner protein and have high biocompatibility. In short, with our elaborately designed millifluidic device, we provide an alternative way to synthesize high-quality protein nanocapsules.