In this paper, micro-structured polymer parts were efficiently and accurately fabricated by micro-injection molding using a micro-structured mold core machined by wire electrical discharge machining (WEDM). The objective was to realize low-cost mass production and manufacturing of micro-structured polymer products. The regular micro-structured mold core was manufactured by precise WEDM. The micro-structured polymer workpieces were rapidly fabricated by micro-injection molding and the effects of the micro-injection molding process parameters on replication rate and surface roughness of micro-structured polymers were systematically investigated and analyzed. It is shown that the micro-structured polymer can be rapidly and precisely fabricated by the proposed method. The experimental results show the minimum size machining error of the micro-structured mold core and the maximum replication rate of micro-formed polymer were 0.394% and 99.12%, respectively. Meanwhile, the optimal micro-injection molding parameters, namely, jet temperature, melt temperature, injection velocity, holding pressure and holding time were 195 °C, 210 °C, 40 mm/min, 7 Mpa and 5 s, respectively. The surface roughness Ra at the groove bottom and top of the micro-structured polymer workpieces achieved minimum values of 0.805 µm and 0.972 µm, respectively.