To solve the thermal management problem in the three-dimensional integrated circuit (3D-IC) with high integration and multilayer, this paper establishes a 3D-IC interlayer microchannel model with various embedded TSV micropin fins to explore the temperature distribution of chips and the flow velocity distribution inside the microchannel. The paper selects the sense amplifier and the half adder as the heat source of the memory and processor in the calculation model. The power densities of the sense amplifier and the half adder are 885 kW/m2 and 1.832 MW/m2 combined with the layout size, respectively. Meanwhile, the effects of the shape and arrangement of TSV micropin fins on the flow and heat transfer characteristics are investigated. The result shows that the 1.2:1 diamond micropin fin microchannel with staggered arrangement has the best overall flow and heat transfer performance. Compared with the basic circular micropin fin with the in-line arrangement, the average Nusselt number of this microchannel is improved by 3.20–3.37 times, and the maximum temperature of chips is controlled at 325.92–312.43 K for Re = 628–1819.