Along with Li-ion extraction/intercalation during charge and discharge processes, structural phase transitions often occur in the electrode materials of Li-ion batteries (LIBs). By determining atomic positions before and after Li adsorptions, structural phase transitions of two-dimensional MXenes were investigated systematically using first-principles density functional calculations. The lithiation-induced phase transitions of ten M₂C MXenes with oxygen groups can be divided into three types. No phase transitions occur for Ti-type MXenes including Ti₂CO₂, Zr₂CO₂ and Hf₂CO₂. The oxygens in Ta-type MXenes (Sc₂CO₂, Y₂CO₂, Nb₂CO₂ and Ta₂CO₂) move from one type of octahedral void to another type of octahedral void. However, for Mo-type MXenes including V₂CO₂, Cr₂CO₂ and Mo₂CO₂, the oxygens move from octahedral voids to tetrahedral voids. The mechanisms whether phase transitions happen or not are dependent on the sizes of M ions. Furthermore, all the predicted phase transitions were confirmed by ab initio molecular dynamics simulations. The calculated results of electron localization functions and Bader charge illustrate that there exist strong Coulomb interactions (ionic bonds) between Li and MXene surfaces. The band structure, diffusion energy barrier, open circuit voltage and storage capacity were calculated to evaluate the lithium storage properties of different MXenes, which reveals that V₂CO₂ and Cr₂CO₂ should be optimal candidates as electrode materials for LIBs.