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To investigate the thermal and flow characteristics in a microchannel with pin fins, numerical simulation is carried out. The influence of variation in fin height is adjudged on thermo-hydraulic performance where the fin height is varied from 0.2 mm to 1 mm and Reynolds numbers from 200 to 1000 with constant heat flux imposed at the bottom of the channel. In general, heat transfer is observed to be significantly increasing with an increase in fin height and Reynolds number. However, heat transfer increases at a similar rate for each cases up to a Reynolds number of 600 but later heat transfer growth for a height of 0.8 mm is found pronounced over that for fin height of 1 mm as the Reynold number continues to increase. This may be attributed to the fact that fin height of 0.8 mm seems to have greater wetted as well as convective surface area as compared to the fin of 1 mm height. Further, available the flow passage around 0.8 mm fin is prone to form vortices much easily as compared to 1 mm fin. The profiles of temperature distribution, pressure drop, and velocity all seem to corroborate this observation.