The increasing need for advanced anode materials with superior performance in rechargeable batteries has driven investigations into cutting-edge energy storage systems. This study delves into the potential of P4Se3 Molecular Cages (MCs) as innovative anode materials for both monovalent and multivalent ion batteries, including Na ion batteries (NIBs), Mg ion batteries (MIBs), Ca ion batteries (CIBs), Al ion batteries (AIBs), and Zn ion batteries (ZIBs) through a comprehensive Density Functional Theory (DFT) and molecular dynamics (MD) based investigations. The analyses encompass the electronic structure, structural stability, electrochemical performance, charge storage mechanisms, and redox properties to offer valuable insights into the potential of P4Se3 as an anode. The DFT calculations unveil critical aspects of adsorption, diffusion, and reaction kinetics in P4Se3 elucidating its potential as high-capacity and suitable anode material. The exothermic reactions between Na, Mg, Ca, Al, and Zn with host P4Se3 highlight its suitability for the intercalation process in monovalent and multivalent ion batteries. Furthermore, calculated storage capacities for NIB, MIB, CIB, AIB, and ZIB are found as 1484.84 mAhg−1, 519.69 mAhg−1, 1410.60 mAhg−1, 593.93 mAhg−1, and 74.24 mAhg−1 respectively. The voltage profiles indicate favorable open circuit voltages (OCV) of 0.31 V, 0.27 V, 0.55 V, and 3.3 V for NIB, MIB, CIB, and AIB respectively. The study employs climbing image nudged elastic band (Cl-NEB) simulations to compute diffusion barriers faced by monovalent and multivalent ions in the host structure. The calculated minimal diffusion barriers of 0.18 eV for NIB, 0.30 eV for MIB, 0.35 eV for CIB, 0.33 eV for AIB, and 0.71 eV for ZIB indicate fast charging capabilities due to efficient ion movement. Furthermore, the respective calculated values of diffusion coefficient are found as 5.27 × 10−10 m2/s, 5.27 × 10−9, 4.0 × 10−10 m2/s, 5.27 × 10−10 m2/s and 5.27 × 10−11 m2/s and respective values of ionic conductivity σ are found as 4.13 × 10−3 S/m, 14.57 × 10−2 S/m, 30.03 × 10−3 S/m, 16.65 × 10−3 S/m and 0.20 × 10−3 S/m for NIBs, MIBs, CIBs, AIBs and ZIBs. The findings of this study point out suitability of P4Se3 as anode material in monovalent and multivalent ion batteries.