The metal/polymer composite microstructure radiator based on the microstructure radiator, has the advantages of small radiating volume, high thermal efficiency, low processing cost, which has a huge market potential in microelectronics, such as LED and high speed microprocessor. In this paper, firstly, the heat transfer process of microstructure heat exchanger was studied using finite element analysis. Then, the metal/polymer composite microstructure heat exchanger was formed using micro-embossing technology, and the influence of pressure applied to the mold on the molding microstructures was explored. Finally, thermal performance testing of the microstructure heat exchanger was conducted. Experimental results showed that, when the slot width was 0.5 mm, with the increase of molding pressure, the aspect ratio of microstructure formed by micro-embossing increased. When the pressure was 2.5 MPa, the aspect ratio was 0.24, however, as the pressure increased to 5 MPa, the aspect ratio rose to 1.26. With the increase of aspect ratio of microstructure, the heat transfer performance of the heat exchanger improved. The thermal performance of cross groove composite microstructure heat exchanger (87 °C) was better than the rectangular groove composite microstructure heat exchanger (90.3 °C). The Experimental conclusions were consistent with the simulation results.