For titanium alloy parts prepared by selective laser melting (SLM), post-treatment operation is usually utilized to meet the needed surface accuracy and dimensional tolerances. However, the heat treatment process and anisotropy of different surfaces of SLMed titanium alloy can directly affect its machinability. In this study, the anisotropic machinability of SLMed TC4 before and after heat treatment was comprehensively compared by the milling force, surface quality, top-burr and work hardening. The results indicate that the milling force and work hardening degree of top surface of SLMed TC4 material are larger than those of side surface, and top surface the presents the better surface quality and smaller top-burr. It exhibits obvious anisotropic machinability in micro-milling. After heat treatment, the anisotropic machinability between different surfaces of SLMed TC4 materials were significantly reduced. The average surface roughness difference rate of top and side surfaces decreased from 10.08% to 2.79%, and the total average top-burr size difference rate decreased from 19.53% to 9.99%. The difference rate of milling force and work hardening degree of the top and side surfaces both showed a decreasing trend. This work demonstrates that the anisotropic machinability of SLMed TC4 material in micro-milling can be effectively mitigated by the heat treatment process.