Structural phase transitions in electrode materials of Li-ion batteries (LIBs) often occur along with Li-ion extraction/intercalation during charge and discharge processes. Lithiation-induced phase transition behaviors of two-dimensional fluorinated MXenes were investigated systematically by first-principles density functional calculations. The calculated results show that fluorine atoms in the nine MXenes studied moved from the FCC site (or HCP site for Ta₂CF₂) to the TOP site during Li adsorption. Further all the predicted phase transitions were confirmed by ab initio molecular dynamic simulations. The band structure, density of state, diffusion energy barrier, average voltage and storage capacity were calculated to evaluate the lithium storage properties of fluorinated MXenes, which revealed that V₂CF₂ and Ti₂CF₂ are the optimal candidates for LIB electrode materials. The structural phase transition led to improvements in the cycle stability, storage capacity, average voltage, and other lithium storage properties of the fluorinated MXenes.