To solve the thermal management problem in the three-dimensional integrated circuit (3D-IC) with high integration and multi-layer, this paper establishes a 3D-IC interlayer microchannel model with various embedded TSV micro-pin fins to explore the temperature distribution of chips and flow velocity distribution inside the microchannel. The sense amplifier and half adder are selected as the heat source of the memory and processor in the calculation model, and the power densities of the circuit modules 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 micro-pin fins on the flow and heat transfer characteristics are investigated. The result shows that the 1.2:1 diamond micro-pin fin microchannel with staggered arrangement has the best overall flow and heat transfer performance. Compared with the basic circular micro-pin 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.