Carbon isotope fractionation served as a key geochemical indicator for understanding shale gas storage and migration. However, the detailed mechanism of the fractionation behaviors of methane isotopes (12CH4/13CH4) was still limited, especially under two-phase flow. This study employed molecular dynamics (MD) simulations to investigate water-mediated nonlinear isotope transport in 3 nm hydrophilic silica nanopores, highlighting gas-liquid-solid interfacial effects on fractionation mechanisms. Simulations of different water saturation (0%–44.66%) showed a critical hydration threshold of 30.44% at a pressure gradient of 20 MPa. Below this threshold, continuous water film formed on pore walls, which transformed the gas transport from surface diffusion to viscous flow through gas-liquid interactions, while hydrogen bonds in the water film weakened gas-solid slip effects. However, when water saturation exceeded 30.44%, the formation of water bridges blocked the mobility of isotopic gases. The water film reduced the depth of solid-gas potential wells, leading to diminished adsorption capacity for isotopic gases, and lowered the surface roughness of pore walls (as characterized by potential energy surface, PES). Additionally, the water film enhanced the Knudsen diffusion effect of isotope gases due to the decrease in effective pore size. As a result, the formation of water film intensified methane isotopic fractionation, which was manifested as a decrease in the 13CH4/12CH4 diffusion coefficient ratio (D∗/D) from 0.975 to 0.942 and an increase in isotopic enthalpy differences (ΔhC12−C13) from 0.105 to 1.139 J/m3. Furthermore, in the gas-liquid-solid interfacial system, an elevated pressure differential modified the relative motion velocities among the methane-water-pore surface, resulting a non-monotonic isotopic fractionation trend (initial increase followed by decrease). These findings provided molecular-level insights into the complex isotopic fractionation in shale gas systems.