Methylmalonyl-CoA epimerase (MMCE) is an enzyme involved in the carbon capturing 3-HP/4-HB cycle, by catalyzing the reaction of converting (S)-methylmalonyl-CoA to (R)-methylmalonyl-CoA. In this study, we overexpressed MMCE from Metallosphaera sedula (MsMMCE) and purified the protein to homogeneity by Ni-NTA affinity and size-exclusion chromatography. The MsMMCE protein was crystallized using the hanging-drop vapor-diffusion method in the presence of 20% (w/v) polyethylene glycol 3350, and 0.2 M ammonium nitrate at 293 K. X-ray diffraction data were collected to a maximum resolution of 2.1 Å. The MsMMCE crystals belong to the space group P2₁ with unit cell parameters a = 51.87 Å, b = 79.00 Å, c = 106.09, α = γ = 90.0°, β = 95.80°. With six molecules of MsMMCE per an asymmetric unit, the crystal volume per unit of protein mass is 2.33 ų Da^–1, which corresponds to a solvent content of approximately 47.13%.