Wettability is a fundamental interfacial property that governs multiphase flow, mass transport, and phase distribution in porous media, thereby influencing hydrocarbon recovery, CO₂ sequestration, shale utilization, and a wide range of subsurface energy systems. Recent developments in molecular dynamics simulations have significantly deepened our understanding of wettability beyond conventional macroscopic phenomena, revealing its molecular basis in surface chemistry, fluid-solid interactions, nanoscale confinement, and interfacial structural ordering. This review synthesizes recent advances in molecular dynamics studies of wettability in porous media and highlights three emerging directions: The molecular origins, characterization, and material dependence of wettability in heterogeneous porous systems; wettability-controlled interfacial transport, nanoscale slip, confined phase behaviour, and multiphase displacement across scales; and multiscale upscaling, data-driven prediction, and the remaining barriers to translating atomistic insights into predictive wettability engineering. It is emphasized that wettability should be regarded as a dynamic and environment-dependent property rather than a static contact-angle metric. Looking forward, the integration of molecular dynamics simulations with multiscale modeling, pore-scale numerical methods, and explainable data-driven approaches is expected to enable predictive wettability engineering in complex porous systems. This review aims to provide a conceptual framework for understanding and controlling interfacial transport in energy-relevant porous materials.