Polyoxometalates (POMs)—well-defined anionic metal–oxygen clusters with tunable redox activity, high acidity, and structural robustness—are promising molecular catalytic units for the selective catalytic oxidation of sulfur-containing compounds, which has broad implications in biomedicine, environmental remediation, and chemical defense. However, the practical use of POMs is frequently hampered by their aggregation and limited recoverability, particularly in polar media. Porous framework materials—metal–organic frameworks (MOFs) and covalent organic frameworks (COFs)—provide structurally precise modular scaffolds for the spatial confinement and stabilization of POMs. The formation of host–guest composites via encapsulation within framework cavities or channel walls not only suppresses POM degradation and leaching but also synergistically enhances active-site accessibility, substrate diffusion and orientation, and interfacial charge transfer kinetics. Existing reviews predominantly focus on single host systems or specific applications (e.g., oxidative fuel desulfurization), failing to systematically encompass all three core research fields. To bridge this gap, the present review comprehensively summarizes recent advances in the use of POM@MOF and POM@COF composites in bioactive sulfide synthesis, fuel desulfurization, and chemical warfare agent decomposition. Correlations between host–guest interactions and catalytic performance, stability, and reaction mechanisms are discussed, and future development directions are prospected to facilitate industrial applications.