Microchannel heat sinks have important applications in integrated circuits, but the current traditional long straight microchannel heat dissipation process causes uneven temperature and low heat dissipation efficiency. In this paper, a periodic split-flow microstructure is designed and integrated with traditional microchannels to form a periodic split-flow microchannel heat sink. Numerical simulation is used to study the influence of the number, the arrangement and structural parameters of microstructures in a single microchannel on its thermal performance. The simulation results show that the split-flow microstructure can increase the heat exchange area, break the original laminar boundary layer, promote the mixing of cold/hot coolant, and significantly improve the heat dissipation performance of the microchannel. Through comparative experiments, 9 groups are finally determined as the optimal number of microstructures in a single microchannel. At a heat flux of 100 W/cm², when the coolant flow rate at the inlet is 1.18 m/s, after 9 groups of microstructures are added into a single microchannel, the maximum temperature drops by about 24 K and the thermal resistance decreases by about 44%. The Nusselt number is increased by about 124%, and the performance evaluation criterion (PEC) reaches 1.465. On this basis, the microstructure adopts a staggered gradual periodic arrangement to avoid the long-distance non-microstructure section between the two groups of microstructures. The turbulence element that gradually widens along the flow direction makes the coolant fully utilized. This results in a reduction in the high/low temperature zone and alleviates the temperature gradient that exists along the flow direction of the heat dissipation surface, and the pressure drop loss is also reduced to a certain extent compared with the pressure drop in the uniform arrangement, and the comprehensive thermal performance is further improved. It shows broad application prospects in the field of high-power integrated circuits and electronic cooling.