A computational fluid dynamics (CFD) model for the Fischer-Tropsch synthesis (FTS) reaction was developed for a compact modular multichannel reactor with microchannel heat exchangers installed between catalytic bed channels. In addition to detailed levels of balance equations, the kinetic parameters for lumped FTS reaction rates and a convective heat transfer coefficient were estimated by fitting experimental data and the validity of model was corroborated by the comparison between experimental and simulated results. The model was used to evaluate the cooling performance of microchannel heat exchangers with varying flow rates, and several reactor specifications including the use of all catalytic bed channels, no inert materials, and reactors arranged in series were considered. When the number of catalytic bed channels was increased, the increase of CO conversion was observed with a maximum temperature within the operating range, but a possible thermal runaway could be expected due to high sensitivity to feed temperature change. In-series reactors also confirmed the increased conversion and the safe operation of the second reactor, and proved to be a major advantage for this reactor arrangement. (C) 2013 Elsevier B.V. All rights reserved.