Abstract: Interlayer microchannel cooling is one of the most promising solutions for 3D stacked chip cooling. In this paper, the effects of two heat source layouts on heat transfer performance of non-uniform heat source 3D stacked chips were analyzed. Then, aiming at the problems of large temperature rise and uneven temperature distribution of heat source 1, which has high overall heat transfer performance, a local encrypted micro-channel structure was proposed to enhance heat transfer. Results show that compared with the uniform microchannel structure, the maximum temperature and maximum temperature difference of the local encrypted microchannel structure are reduced by 25.4 K and 15.6 K, respectively. When the pump power is 0.185 W, the thermal resistance of the local sealing structure is reduced by 31%. At the same time, the flow rate corresponding to the local encryption structure is only 180 mL/min, while the flow rate corresponding to the uniform microchannel structure is 225 mL/min. While strengthening heat transfer, the encrypted structure can reduce the flow required for heat dissipation and reduce the load of the cooling system, which is very meaningful in practical applications.