Heat transfer capacity of compact heat exchanger is critical for applications with confined space and with large heat duty, in order to maintain the safety and efficiency of equipment. As a high-efficient and energy-saving compact heat exchanger, microchannel heat sinks have attracted extensive attention from both academics and industries. However, the development of thermal boundary layer in microchannel reduces the efficiency of heat transfer. Therefore, extensive efforts have been paid to improve the heat transfer performance in microchannel, for example, through incorporation of periodic rough elements of pin-fin, groove, rib and protrusion, which could disrupt the development of thermal boundary layer and induce secondary flow for thorough mixing between near-wall hot fluid and main fluid. Despite of superiority in the microchannel heat sink with protrusion, further structural optimizations are necessary to reduce resistance and enhance the heat transfer efficiency. Investigations on the flow resistance of shark, as well as the geometry of sharkskin, show that the discrete gap and hump of sharkskin reduce the flow resistance. Therefore, the split protrusion was proposed in this work, which was based on the common protrusion and shark skin bionic concept. And, the detailed flow structure and heat transfer mechanisms of microchannel heat sinks with split protrusion were studied. Transitional periodic boundary conditions were applied at the inlet and outlet with water as the working fluid, and the Reynolds number (Re) at the inlet were varied from 50 to 350. Moreover, a uniform constant heat flux of q′′ =5×105 W m−2 and no-slip boundary condition were specified at other surfaces of the microchannel. Furthermore, to avoid local hot spot of microchannel surfaces due to the existence of non-uniform temperature distribution, the temperature uniformity was discussed as well. The results show that thermal performance ( TP ) increases with the increase of Re and the superior heat transfer capacity is reached when the split width is 10 μm. In this study, the largest TP is 185.3% at the case of Plan A with Re=350 and 10 μm split width, where the relative friction factor ( f / f 0) is much large. As the width of split increases to 15 μm in Plan A, its f / f 0 significantly decreases but the thermal performance is relative large. Moreover, f / f 0 is also smaller than others at the case of PlanB with 15 μm width split. For Plan B with large split width, the value of TP increases with the split width at large Re (>250), while there is an opposite trend with the split width at small Re ( w / D ). Keeping other conditions at the same, the TP for Plan A is larger than that for Plan B when w / D is larger, while the f / f 0 is relatively smaller in PlanB at the case of smaller w / D , especially for the cases with wide split passage . However, the f / f 0 in PlanC with the smaller w / D is much larger than that of others, especially at large Re, since the sideward-inclined split in PlanC guides the part of main flow to side walls, enhancing the secondary passage flow of whole channel. Therefore, the temperature of side wall corners has been decreased effectively and the temperature uniformity of all walls in Plan C increases.