Understanding the phase equilibria and physical-chemical characteristics of the CH4–CO2–H2O–NaCl quaternary system is important for evaluating costs and risks for the storage of CO2 in depleted natural gas reservoirs as well as fluid inclusion studies. In this study, phase equilibria and thermodynamic properties of this system were investigated through the utilization of a statistical association fluid theory-based (SAFT) equation of state (EOS) at temperatures from 298 to 513 K (25–240 °C), pressures up to 600 bar (60 MPa) and concentration of NaCl up to 6 mol/kgH2O. The model parameters were obtained from the fitting of available experimental data of subsystems (i.e., CH4–H2O, CH4–CO2, and CH4–H2O–NaCl) that were judged to be reliable and incorporation of available parameters for the subsystems (i.e., pure component, CO2–H2O, and CO2–H2O–NaCl). Using the SAFT EOS developed in this study, we predicted the solubility of (CH4 + CO2) gas mixtures in pure H2O and compared it with the available experimental data and the predicted values from four popular numerical simulators. The results indicate that our model can provide reliable predictions for the CH4–CO2–H2O ternary system. Subsequently, we further predicted the phase equilibria and density of the CH4–CO2–H2O–NaCl system with NaCl varying from 0 to 6 mol/kgH2O. We also employed the SAFT EOS to predict the solubility of CO2 and CH4 in the water-alternating-gas process for CO2-enhanced oil recovery, demonstrating good agreement with the simulation results obtained through the Peng-Robinson EOS for predicting the CO2 and CH4 solubility. These predicted thermodynamic properties and phase behaviors in the CH4–CO2–H2O–NaCl system provide quantitative insights into the implications of CO2 storage in depleted oil and gas reservoirs.