Zeolite Y has been considered as one of the most versatile materials that are used in catalysis, adsorption, and separation. However, its inherent microporosity often impedes the diffusion of reactants and products, thus constraining overall performance. This review systematically investigates the major post-synthetic modification strategies intended to mitigate these limitations and to refine the structural and physicochemical properties of zeolite Y. Particular focus is placed on the mechanisms and structural consequences of dealumination, desilication, ion exchange, and surface functionalization, each of which uniquely influences acidity, porosity, and framework stability. The synergistic combination of dealumination and desilication is especially highlighted for its capacity to generate hierarchical structures containing mesoporosity with optimal acidity robustness. Recent developments that integrate the use of microwave and ultrasound-enhanced methods are considered sustainable and energy-efficient solutions that offer accurate control over the framework transformation and shorten processing times. These post-synthetic advancements have led to hierarchical, multifunctional zeolite Y materials that show high levels of catalytic activity, enhanced adsorption capacity, and improved selectivity over a wide range of industrially related reactions. This review concludes how such modification techniques expand the functional range of zeolite Y, thereby enabling its use in new areas of application, including CO2 capture, biofuels production, and environmentally friendly catalytic processes. Future perspectives emphasize ongoing refinement of structure-function relationships, scalability of processes, and integration of modification methodologies to reinforce zeolite Y’s pivotal role in sustainable chemical manufacturing.