<p>The efficient separation and regulation of immiscible oil–water mixtures remain a persistent challenge in petrochemical processing, lubrication systems, wastewater treatment, and microfluidic devices. Experimental approaches provide macroscopic observations but are limited in resolving the coupled hydrodynamic, interfacial, and thermo-mechanical mechanisms governing confined multiphase flows. In this work, a unified multiphysics computational framework is developed to investigate pore-scale transport within bioinspired honeycomb membranes incorporating temperature-dependent material properties, sorption-controlled interfacial mass transfer, thermoelastic wall deformation, and phase-field interface dynamics. The governing equations for momentum, species transport, structural mechanics, and interface evolution are solved in a fully coupled manner. Model validation against experimental breakthrough data shows deviations below 4.6%. Thermo-mechanical compliance reduces mixing length by approximately 18% compared to rigid-wall conditions. Results demonstrate that temperature-induced wall softening and thermal expansion significantly modify pressure distribution, interfacial stress, and solute flux. The phase-field formulation accurately captures bubble deformation, migration, and coalescence, while deformation–Capillary number scaling quantifies viscous–capillary competition under structural compliance. Unlike previous pore-scale simulations assuming rigid and isothermal boundaries, the present study simultaneously integrates temperature-dependent viscosity and density, thermoelastic deformation, sorption-controlled mass transfer, and diffuse-interface modeling. This comprehensive framework provides predictive insight for the design of advanced membranes, lubrication systems, and microreactors with tunable transport performance.</p> Graphical abstract <p></p>