Through-silicon via (TSV) technology offers significant advantages for three-dimensional integrated chip (3D-IC) by enabling higher integration densities and faster signal transmission rates. The increased power density of 3D-IC poses substantial thermal management challenges. Microchannel cooling is widely used for chip-level thermal management. However, the balance of heat dissipation and signal integrity between layers of 3D-IC with TSV remains elusive. This work presents a study on the electrical-thermal-force-flow-solid multi-physics field coupling effect of micro pin–fin channel cooling systems embedded with coaxial-like TSVs in 3D-IC, aiming to optimize signal integrity and thermal performance. We analyze the structural parameters of coaxial-like TSVs, such as TSV aspect ratio and pitch ratio, focusing on their impact on signal shielding efficiency and thermal conductivity. The results show that a coaxial-like TSV structure with an aspect ratio of 15 and a pitch ratio of 2.5 reduces the maximum temperature and insertion loss by 3.97% and 3.60%, respectively. This structure is then embedded in a micro pin–fin channel to explore the effect of pin–fin arrangement on heat dissipation at different Reynolds numbers. Using multi-objective optimization through response surface methodology (RSM) and the non-dominated sorting genetic algorithm II (NSGA-II), we obtain a series of optimal solutions for TSV-embedded micro pin–fin. When the weights of heat transfer and pressure drop are balanced, the average Nusselt number increases by 6.8% with a 2% rise in pressure drop. These findings provide valuable insights for the design and optimization of high-performance 3D-IC cooling systems.