Abstract: Groundwater, as a globally strategic freshwater resource, plays a critical role in ecosystem stability, targeted pollution remediation, and geothermal energy development. Its migration mechanisms directly influence decision-making in these major engineering fields. However, natural porous media—such as aquifer sands, gravels, and fractured rock formations—generally exhibit heterogeneous topological structures and pronounced multiscale effects, resulting in complex nonlinear behaviors in subsurface multiphase flow. Traditional hydrological observation methods are limited by spatial resolution and thus struggle to reveal flow mechanisms and interaction processes at the pore scale. To overcome these limitations, this study develops a non-invasive, in situ visualization experimental platform integrating high-resolution computed tomography (CT) scanning and microfluidic chip technology, achieving micron-scale spatial resolution for dynamic observation and quantitative characterization of multiphase flow in porous media. The experimental system systematically measures fluid saturation distribution, interface morphology evolution, and capillary pressure changes within pore structures. The results indicate that: (1) Wettability, as a key parameter controlling multiphase flow behavior, exerts regulatory effects throughout the entire process—from pore-scale fluid distribution and interface morphology evolution to core-scale flow responses. By adjusting wettability, the spatial migration pathways and interfacial mechanical states of fluids in sandy porous media are significantly altered, triggering interface structure reconstruction and connectivity changes. These microscale processes directly impact displacement efficiency and residual fluid distribution patterns, ultimately leading to pronounced differences in relative permeability response characteristics. (2) Under varying wettability, viscosity ratio, and flow rate conditions, multiphase flow exhibits diverse flow regimes and energy conversion characteristics. Wettability, flow velocity, and viscosity synergistically regulate interface stability and the power–energy transfer pathways; notably, in the critical transition zone from capillary-dominated to viscous-dominated flow, external work input markedly increases and interfacial energy fluctuates sharply. Additionally, this work assesses the advantages and technical challenges of the combined CT-microfluidic technique in multiphase flow studies. The findings provide key microscopic mechanistic support for engineering issues such as groundwater pollution remediation and enhanced multiphase flow efficiency, demonstrating broad application potential of non-invasive high-resolution experimental methods in environmental and energy engineering.