Understanding the transport of nanoconfined fluid and its underlying mechanism is essential for manipulating fluid transport in nanochannels and nanoporous media. The wettability of the channel wall is one of the most important factors that determine the property and transport of nanoconfined fluid. However, the experimental studies of wettability adjustment for manipulating nanofluid transport were rarely reported. In this work, the wettability of nanochannels in nanofluidic chips was tuned in situ to investigate the transport of water and alkane. The surface hydrophobicity of the channel wall was adjusted through hydroxylation and silanization. The friction factor of water increased with the hydroxylation time of the channel wall, and decreased after surface hydrophobization with octadecyltrichlorosilane (OTS) and trimethylchlorosilane (TMCS), indicating surface hydrophobization had a significant effect on friction reduction. The linear correlation between the transport distance ΔX2 and time t could be theoretically described based on the Lucas-Washburn equation for fully developed flow. With the same channel depth, the fitted apparent contact angle θapp for nanochannels of different hydrophobicity followed the trend of OTS > TMCS > pristine > hydroxylation. The transport of water in hydrophobized nanochannels was faster than that in pristine and hydroxylated nanochannels, which coincided with the friction factor results. The transport of n-hexane was significantly faster than that of water, which could be explained by the differences in the fluid viscosity, surface tension and wettability. This work provides experimental evidence and useful insights into the understanding of the wettability effect of nanochannel on the transport of different fluids, which has implications for the transportation characteristics of nanoconfined fluids in the applications, such as advanced batteries, separation membranes, unconventional reservoirs, etc.