In this research, thermal analysis is performed numerically to investigate the performance of microchannel with different protrusions. Four different configurations of circular protrusions are considered to simulate by computational fluid dynamics. The deionized water has been utilized as working fluid in this research, so that its thermal‐physical properties are dependent on temperature. The finite volume approach is employed for solving the governing equations of the laminar fluid flow in steady state condition. The outcomes of the numerical simulation show a very good agreement compared to experimental data. It can be found that the employing protrusions on the bottom wall impresses the thermal criteria in microchannels. The influence of protrusions on the heat transfer coefficient and the ratio of Nusselt number changes compared to the smooth channel are evaluated at various velocity of the fluid. An important result is that the microchannel with higher radius of protrusions has a better heat transfer rate.