The role of phase topology in hysteresis during fluid injection and withdrawal in porous media is not fully understood. We address this by providing experimental and theoretical evidence on three key findings. (1) The topological evolution of the nonwetting fluid is distinct from capillary pressure and specific interfacial area, with the Euler characteristic not bounded by main imbibition and drainage curves, as shown by experiments and a generalized model. (2) Saturation paths with identical capillary pressure and interfacial area show different topologies, revealing insights into energy dissipation and phase connectivity. (3) The topological evolution of the nonwetting phase follows predictable, convex set interactions, captured by a piecewise nonlinear model. These findings offer practical implications for designing subsurface hydrogen and carbon dioxide storage systems and provide a novel approach for studying complex systems with topological singularities.