A numerical analysis is conducted on flow and heat transfer of different configurations of miniature chamber with and without the rectangular pin as complex and smooth models, respectively. Five configurations of the miniature chamber are considered, and they are named for short as smooth models, including RC, HC1, TC1, HC2, and TC2, and complex models, including RC-RP, HC1-RP, TC1-RP, HC2-RP, and TC2-RP. Experiments are also carried out on a real straight case in order to validate the numerical results and create a baseline for the comparison. The working fluid is water in the laminar flow regime. It is found that the numerical results are in a good agreement with the current experimental data, whose the maximum differences are 5.3% for the heat transfer coefficient and 6.4% for the pressure drop. Depending on the studied case and Reynolds number (400 < Re < 1990), the Nusselt number and friction factor are 0.85–1.95 and 0.45–10.66 times as compared with those for the straight baseline model, leading to the performance index of 0.77–1.54. The results indicate that the complex models have better heat transfer performance with a certain pressure drop as compared to the smooth models. It can attribute to enlarging of surface area, increasing of fluid mixing, interrupting and redeveloping of boundary layers, etc. This study can provide efficient findings for thermal engineers working on microelectronic cooling systems.