The electrochemical reduction of carbon dioxide (CO2RR) represents a promising approach for the sustainable production of value-added chemicals from CO2. However, maintaining long-term operational stability under industrially relevant high current densities remains a major challenge, primarily due to electrolyte flooding and carbonate precipitation, which severely compromise the performance of gas diffusion electrodes (GDEs). In this study, we present an advanced gas diffusion layer (GDL) design incorporating multi-walled carbon nanotubes (CNTs) into porous carbon-based microporous layers (MPLs). The resulting architecture facilitates the formation of a continuous, hydrophobic CNT–polytetrafluoroethylene (PTFE) network via preferential PTFE alignment along the CNT surfaces. This hydrophobic CNT-PTFE network effectively mitigates electrolyte flooding while maintaining efficient gas transport pathways. As a result, the CNT-reinforced GDE demonstrated substantially enhanced CO2RR performance, sustaining a CO Faradaic efficiency above 80% for 50 h at a current density of 400 mA cm−2. In contrast, conventional carbon-based GDEs exhibited rapid performance decay within 10 h under same conditions. These findings highlight that microstructural engineering of the GDL, via the formation of a hydrophobic CNT–PTFE network, provides a robust and scalable strategy for enhancing flooding resistance and operational durability in CO2RR systems.