A carbon nanotube (CNT) may facilitate near-frictionless water transport within it. In this work, we elucidate the slip flow characteristics for a CNT embedded in a silicon nitride matrix using the molecular dynamics (MD) method. We reveal that the wetting transparency of a CNT, the transmission of the membrane matrix wetting property over a CNT, cannot be ignored. Due to the effect of CNT wetting transparency, the orientation flip behavior of water molecules should be the primary cause of the entrance and exit losses, which is a dominant factor influencing the interfacial friction coefficient for the thin CNT membrane. The relationship between the friction coefficient and pore size follows a logarithmic function, which agrees well with the reported experimental data. Our findings bridge the gap between the MD prediction and experimental observation for water transport in a CNT membrane and provide a clear understanding of the mechanism behind its ultrafast flow performance.