The main goal of the considered work is to adjust mathematical modeling for mass transfer, to specific conditions resulting from presence of chemical surface reactions in the flow of the mixture consisting of helium and methanol. The thermocatalytic devices used for decomposition of organic compounds incorporate microchannels coupled at the ends and heated to 500 ◦C at the walls regions. The experiment data were compared with computational fluid dynamics results to calibrate the constants of the model’s user defined functions. These extensions allow to transform the calculations mechanisms and algorithms of commercial codes adapting them for the microflows cases and increased chemical reactions rate on the interphase between fluid and solid, specific for catalytic reactions. Results obtained on the way of numerical calculations have been calibrated and compared with the experimental data to receive satisfactory compliance. The model has been verified and the performance of the thermocatalytic reactor with microchannels under hydrogen production regime has been investigated.