Metal-organic framework/organosilica hybrid membranes on tubular ceramic substrates have shown great potential for the implementation of membrane technology in practical gas separation projects due to their higher permeance compared to commercial polymers. However, the selectivities of the reported membranes are moderate. Here, we have incorporated urea-modulated metal-organic frameworks into organosilica membranes to greatly enhance its separation performance. The urea-modulated metal-organic frameworks exhibit less-defined edges of crystallographic facets and high defect density. They can be well-dispersed in the organosilica layer, which substantially suppresses the interfacial defects between metal-organic frameworks and organosilica, which is beneficial for improving the selectivity of membranes for gas separation. The results have shown that the enhanced ideal selectivity of H₂/CH₄ was 165 and that of CO₂/CH₄ was 43, with H₂ permeance of about 1.25 × 10⁻⁶ mol·m⁻²·s⁻¹·Pa⁻¹ and CO₂ permeance of 3.27 × 10⁻⁷ mol·m⁻²·s⁻¹·Pa⁻¹ at 0.2 MPa and 25 °C. In conclusion, the high level of hybrid membranes can be used to separate H₂ (or CO₂) from the binary gas mixture H₂/CH₄ (or CO₂/CH₄), which is important for gas separation in practical applications. Moreover, the simple and feasible modulation of metal-organic framework is a promising strategy to tune different metal-organic frameworks for membranes according to the actual demands.