This work investigated the long-term hydrothermal performance of composite carbon-SiO2-ZrO2 membranes. A carbon-SiO2-ZrO2 composite was formed from the inert pyrolysis of SiO2-ZrO2-polybenzoxazine resin. The carbon-SiO2-ZrO2 composites prepared at 550 and 750 °C had different surface and microstructural properties. A carbon-SiO2-ZrO2 membrane fabricated at 750 °C exhibited H2 selectivity over CO2, N2, and CH4 of 27, 139, and 1026, respectively, that were higher than those of a membrane fabricated at 550 °C (5, 12, and 11, respectively). In addition to maintaining high H2 permeance and selectivity, the carbon-SiO2-ZrO2 membrane fabricated at 750 °C also showed better stability under hydrothermal conditions at steam partial pressures of 90 (30 mol%) and 150 kPa (50 mol%) compared with the membrane fabricated at 500 °C. This was attributed to the complete pyrolytic and ceramic transformation of the microstructure after pyrolysis at 750 °C. This work thus demonstrates the promise of carbon-SiO2-ZrO2 membranes for H2 separation under severe hydrothermal conditions.