•Nanofluids own better heat transfer performance than Ar base fluid.•Nanofluids with higher volume concentration have superior heat transfer capability.•Brownian motion and spinning motion of nanoparticles facilitate heat transfer.•Deposited nanoparticles can act as nano fins and extend low potential energy region. Nanofluids have been proved to be novel work fluids with preeminent thermophysical properties to improve the heat dissipation of the micro/nanochannel. Here we provide atomistic insights into heat transfer and flow behaviors of nanofluids in nanochannels using molecular dynamics simulation. Nanoparticles are found to possess suspension and deposition statements during the flow process in the nanochannel. The temperature development can be accelerated and the temperature jump occurs at the wall-fluid interface in nanofluids. The velocity of the near-wall fluid is disturbed by deposited nanoparticles. In comparison with the base fluid, nanofluids can promote the heat transfer and the nanofluid with a higher nanoparticle volume concentration owns the better convective heat transfer performance. It is discovered that nanoparticles with the irregular Brownian motion and spinning motion disturb the fluid flow and intensify collisions among fluid atoms and thus enhance the heat transfer of nanofluids. Deposited nanoparticles act as nano fins to increase heat transfer areas and disturb the near-wall fluid flow, which ameliorates the convective heat transfer of nanofluids in the nanochannel.