In microreactor systems, concentration distribution is deformed by secondary flow when a fluid passes a join, bend, or bifurcation section in a microchannel. If flow is laminar and steady, a mapping matrix can be defined and it transforms an inlet concentration vector to an outlet one. This transform matrix can be constructed of only the flow velocity information. However, it is generally difficult to find the transform matrix that satisfies rigorously the mass conservation condition. To overcome this difficulty, a new algorithm has been developed. In the procedure, a diffusion equation for the deviation from conservative law is utilized to relax the local errors. To evaluate the present algorithm, the outlet concentrations in the channel joining sequentially with five branches were calculated and the results were compared with the experimental ones.