A novel composite elliptic pin-fin microchannel heat sink (CEP-MCI IS) for the cooling of high heat flux devices is presented in this paper. The thermal performance of the novel heat sink is compared with the other three kinds of structures [a smooth microchannel heat sink (MC:HS), a cylindrical pin-fin microchannel heat sink (CP-MCHS), and an elliptical pin-fin microchannel heat sink (EP-MCHS)] using the numerical simulation approach under laminar flow conditions (250 <= Re <= 850). It is found that CEP-MCI IS has the best performance in heat dissipation and temperature uniformity, which is attributed to flow disturbance and boundary layer damage. When the Reynolds number (Re) reaches 850, the average Nusselt number of CEP-MCHS is 33, which is roughly 1.5 times of CP-MCHS and EP-MCHS and 2 times of MCHS. Besides, a dimensionless parameter Te is introduced to evaluate the substrate temperature uniformity. The total thermal resistance of CEP-MCI IS is the lowest at the same pump power. Moreover, CEP-MCHS has lower entropy generation under the same working conditions than MCHS, CP-MCHS, and EP-MCHS. Conclusively, the CEP-MCHS has an excellent comprehensive thermal management performance. Finally, the structure of CEP-MCHS is further optimized to achieve its best heat dissipation performance.