Based on the molecular dynamics principle, the convective heat transfer of the fluid through nanochannel with various rough nanostructure morphologies is investigated. The influences of nanostructure free shear ratio, morphology period and nanostructure depth on the flow and heat transfer characteristics are probed. A comprehensive evaluation on the convective heat transfer in rough nanochannel considering the flow resistance is performed. The result shows that the temperature jump and velocity slip dominate the heat and momentum exchange between the channel wall and fluid. Under the weak wall-fluid interaction, the smaller the nanostructure free shear ratio, the better the heat transfer performance as well as drag reduction characteristic. In contrast, the smaller the nanostructure morphology period, the better the heat transfer performance, the greater the flow resistance. Therefore, the wall rough morphology with small free shear ratio and sparse nanostructures is conducive to heat transfer augmentation and drag reduction jointly. The deeper rough nanostructure groove is unfavorable to reduce the flow resistance. The combination of rough nanostructure morphology and weak wall-fluid interaction is crucial, which will bring about a favorable impact on the heat transfer and flow resistance in nanochannel. Specifically, the nanostructure free shear ratio with a=0.1875 is a favorable rough morphology to obtain optimum heat transfer and drag reduction characteristics in nanochannel. © 2021 Elsevier Masson SAS