Microchannel-based chemical reactor is widely used to develop chemical products. High-efficiency reactors are required to produce high-quality chemical products. The reaction efficiency is highly related to the mixing ratio. In this paper, an inner structure model in the reactor was designed to improve the mixing ratio. Computational fluid dynamic (CFD) analysis was carried out for two-phase flow in a continuous flow reactor using a commercial software. A case model of the different inner structures was designed to evaluate the mixing rate. Velocity profiles, mixing ratio, and pressure fields of each model were obtained by two-fluid flow analysis using CFD. Based on the analysis results, a reactor model with a high mixing ratio was selected. Powder bed fusion based metal additive manufacturing process was performed to manufacture the 3D microchannel-based chemical reactor. It is expected that the proposed reactor could be applied to a high-efficiency reactor system to produce various chemical materials. For instance, it was possible to perform a chemical reaction based on a toxic material, such as, dimethylformamide solution, using the proposed 3D metal microchannel-based reactor.