The heat transfer enhancement of a jet issued from the circular cylinder placed in a three-dimensional microchannel at low Reynolds numbers were studied systematically by using the numerical simulation. The effects of the jet on thermal efficiency were evaluated by varying injection ratios (I) and jet angles (θ). The physical mechanism of heat transfer was revealed through the analyses of vorticity dynamic and temperature field. The results showed that the thermal efficiency was proportional to the injection ratio at Re = 100 and 200. However, at Re = 300, the thermal efficiency did not increase monotonically with the injection ratio, and the local maximum value of heat transfer efficiency, slightly less than the highest thermal efficiency, appeared at I = 1.5. This was a result of the jet inducing the vortex generated on the cylinder to become unstable. Furthermore, the change of jet angle had a better effect on heat transfer performance compared to the increase in the injection ratio. The separation point of the flow over cylinder and the vortices in the near field were adjusted by the change in jet angle. At the appropriate range of the jet angle, the wake vortices in the near field transitioned from quasi-steady to unsteady in the far field. The instability of wake vortices can disturb the thermal boundary layer near the wall so as to improve the heat transfer performance.