Abstract: Flue-gas co-injection with steam is an effective pathway for green and efficient heavy-oil development. Elucidating its enhancement mechanisms at the molecular scale can accelerate large-scale field deployment. In this study, a three-phase molecular dynamics model of heavy oil–steam–flue gas was established to examine interfacial interactions under varying temperature, pressure, and gas oil ratio. The results show that as temperature increases from 323 to 423 K, the diffusion coefficient of flue gas and the volumetric expansion coefficient of crude oil rise by 4.2-fold and 1.6-fold, respectively. Higher temperature strengthens the thermal motion and diffusivity of flue-gas molecules, effectively disrupting the associations among heavy fractions such as resins and asphaltenes. Above the saturation pressure, gas molecules can overcome mass-transfer resistance, enhancing solubility and thereby promoting viscosity reduction. Increasing the gas co-injection dosage enables more molecules to insert into intermolecular gaps, weakening strong interactions (e.g., π–π stacking) and consequently intensifying penetration, swelling, and dilution of the heavy oil.