A novel phospho‐based hydrophobic deep eutectic solvents (HDESs) is proposed to selectively extract valuable metals from waste lithium‐ion batteries (LIBs). Under the optimized extraction conditions, the single‐stage extraction efficiency of HDES [TOP][Lid] for Co2+ and Ni2+ were 98.5% and 83.9%, and HDES [TBP][Lid] for Co2+ and Ni2+ were 96.0% and 82.9%, and Li+ was enriched in the extract. FT‐IR, 1H NMR, and ESP analysis confirmed the hydrogen bond between HBD and HBA. The metal ion extraction mechanism by HDESs was analyzed based on quantum chemistry (QC) and molecular dynamics (MD). The extraction mechanism at the molecular level is that electrostatic and coordination interactions between transition metal ions and HDESs dominate the extraction of metal ions (Co2+ and Ni2+). The interaction intensity with HDESs was stronger than that between Li+ and HDESs.