Magnesium ion battery (MIB) has gradually become a research hotspot because of a series of advantages of environmental protection and safety. Still, magnesium ion battery lacks cathode materials with high energy density and rate capacity, which influences the electrochemical properties of magnesium ion battery. This paper selects KMnO4 as an oxidant and the divalent salt of Mn2+ as a reducing agent. The α-MnO2/Ti3C2, β-MnO2/Ti3C2, and γ-MnO2/Ti3C2 were prepared by means of hydrothermal synthesis; at the same time, the ratio of MnO2 and Ti3C2 was adjusted. The effects of the different crystal structures of MnO2 on the microstructure and electrochemical properties of MnO2/Ti3C2 composites with different proportions were studied. The results show that the MnO2 crystal structure has a significant influence on the microstructure of the electrode material. The α-MnO2 is uniformly distributed in the composite, providing more transmission paths for magnesium ions. Besides, we found that when α-MnO2 and Ti3C2 are in the proportion of 1:2, the electrochemical performance is optimal, and its capacity can reach 125 mA h g−1, which is 140% of the γ-MnO2 crystal structure.