Velocity uniformity in reaction channels has a significant effect on the performance of laminated microreactors with micro-pin-fin arrays (MPFAR) for hydrogen production. The hydrogen production efficiency can be improved by optimizing the structure of flow manifolds. The relationship between the flow manifold structure and the velocity distribution in the reaction channel with MPFAR is established by an equivalent electrical resistance network model validated via simulation. The effects of the flow manifold structure on the velocity distribution are investigated. The results show that the velocity distribution can be improved by increasing the y-direction coordinate Y-pi of the flow manifold inlet tube. The flow manifold structure is optimized for better velocity distribution in reaction channels with different MPFAR widths.