As flexible heat dissipation devices are urgently needed for flexible electronics, polymers with the advantages of good flexibility, insulation, and low density have attracted wide attention. It would be interesting to fabricate thermal functional structures on polymers to overcome their low thermal conductivity. This study aims to design and fabricate a micro-embossing mold to process polymer three-dimensional microgroove wicks (3D-MWs), which are applied in flexible heat pipes and achieve high thermal conductivity. Three kinds of tungsten steel molds were processed by using two wire electrical discharge machining processes (WEDM), two electrical discharge shaping machining processes (EDSM), and a combination of WEDM and EDSM. The 3D-MWs of the tungsten steel mold were reprinted onto the polymer films by a two-step embossing process. To investigate the effects of microstructures on boiling heat transfer performances, tungsten steel molds fabricated by different methods were tested to reflect the heat dissipation potential of the polymer 3D-MWs. The results showed that the 3D-MWs fabricated by the combination of WEDM and EDSM exhibit good boiling heat transfer performance and high processing efficiency, with a critical heat flux of 1040.1 kW/m2 and a maximum heat transfer coefficient of 38.4 kW/m2·°C. These values are 46% and 611% higher than those of the smooth tungsten steel surface, respectively, making it a superior choice for micro-embossing molds.