Superswells and domes—large-scale, persistent interface deformations—are key features in geophysical and multiphase systems driven by thermal convection. These structures often emerge in layered convective systems, such as Earth's mantle or two-fluid industrial processes, where buoyancy contrasts and fluid properties create complex interface dynamics. However, the physical mechanisms governing the formation of these structures remain poorly understood. Here, we use high-resolution direct numerical simulations of two-layer Rayleigh–Bénard convection to investigate how the Prandtl number Pr and buoyancy number B govern transitions in interfacial morphology. At a fixed Rayleigh number Ra, we identify three distinct regimes: stratified convection at high $B$, where buoyancy suppresses interfacial motion; an interfacial fragmentation regime at low Pr and B, driven by inertial–buoyant balance; and a dome-forming regime at high Pr, where viscous and buoyant forces deform the interface into coherent, superswell-like structures. A theoretical phase diagram predicts these transitions and agrees well with simulation results. These findings provide mechanistic insight into interfacial phase behavior in thermally driven flows, offering a framework that links geophysical surface features with underlying convective dynamics and informing the control of interfacial morphology in complex multiphase systems.