In this study, numerical simulations are conducted to investigate the effects of initial models (parallel and symmetrical arrangement) using interruption fins on the flow and heat transfer characteristics of microchannel heat sink (MHS). The results indicate that MHS with symmetrical fin arrangement has a higher Nusselt number and lower thermal resistance. The vortices perpendicular to the flowpath is the main factor of affecting the heat transfer characteristics. Because of the higher vorticity, the channel with symmetrical fins achieves higher heat transfer performance. To further improve the heat transfer performance, three modified models (models III–V) are obtained by adopting the methods of staggered, reducing fin quantity, and adding pin fins, respectively. The staggered arrangement of fins can deepen the secondary flow in the channel, and the additional vortices are formed with adding pin fins, which can enhance heat transfer capacity in models III and V. On the other hand, reducing the number of fins can damage some vortices, which can actually reduce heat transfer performance. It is worth noting that both the staggered fins and the pin fins significantly increase the pressure drops of the channel, while reducing the fins number leads to an obvious decrease in the pressure drop.