Owing to continuing global use of lithium-ion batteries (LIBs), in particular in electric vehicles (EVs), there is a need for sustainable recycling of spent LIBs. Deep eutectic solvents (DESs) are reported as “green solvents” for low-cost and sustainable recycling. However, the lack of understanding of the coordination mechanisms between DESs and transition metals (Ni, Mn and Co) and Li makes selective separation of transition metals with similar physicochemical properties practically difficult. Here, it is found that the transition metals and Li have a different stable coordination structure with the different anions in DES during leaching. Further, based on the different solubility of these coordination structures in anti-solvent (acetone), a leaching and separation process system is designed, which enables high selective recovery of transition metals and Li from spent cathode LiNi1/3Co1/3Mn1/3O2 (NCM111), with recovery of acetone. Recovery of spent LiCoO2 (LCO) cathode is also evidenced and a significant selective recovery for Co and Li is established, together with recovery and reuse of acetone and DES. It is concluded that the tuning of cation–anion coordination structure and anti-solvent crystallization are practical for selective recovery of critical metal resources in the spent LIBs recycling.