We specially designed a slow chemical reaction system to synthesize the zinc selenide nanoparticles (ZnSe NPs), in the cavity of the cage-shaped protein, apoferritin. The newly designed chemical synthesis system for ZnSe NPs makes the chemical reaction of compound semiconductor element ions dramatically slow, resulting in that ZnSe NPs can be synthesized in the internal cavity of the apoferritin. The ZnSe NPs synthesized by the optimized reaction parameters are efficiently produced in the aqueous solution. The UVVis spectrum analysis of synthesized ZnSe-ferritin suggests that the formation of ZnSe nuclei in the apoferritin cavity takes about 6 hours by using our slow chemical reaction system. The synthesized ZnSe NPs were characterized by high resolution TEM, X-ray powder diffraction (XRD) and Energy Dispersive Spectrometory (EDS) and it was revealed that the synthesized NPs are a collection of cubic ZnSe crystals.