With the development of higher performance and miniaturization of electronic components, the flow heat transfer of working fluids in nanochannels has received more attention. To elucidate this phenomenon, molecular dynamics simulations are used to simulate the behaviors of fluids within nanochannels at temperatures of 300 K, 325 K, and 350 K. Water serves as a flow medium, with argon substituted for any non-condensable gases. In the flow process, argon atoms aggregate into clusters that are characterized by high potential energy. As the temperature rises, the concomitant increases in the fluid’s potential energy, which leads to the gradual diminution or complete dissipation of these clusters. A minor presence of gas atoms can facilitate fluid movement; however, an excess of argon promotes the formation of larger gaseous clusters in the central region of the channel, thereby impeding fluid flow. Concurrently, the application of heat to the fluid appreciably diminishes the coefficient of flow resistance. The temperature of the fluid in the near-wall region exceeds that of the central area. In the clusters, the atoms exhibit heightened activity, leading to an increase in the average molecular kinetic energy and a concomitant rise in temperature. The inherent hydrogen-bonding structure of water enhances heat transfer within the nanochannels. Argon atoms exert an influence on the number of hydrogen bonds, and rising temperatures disrupts the hydrogen-bond network established by water molecules, ultimately leading to a decrease of the Nusselt number. This investigation offers insights into the heat transfer dynamics of water molecular flow within microchannels under the perturbation of non-condensable gases, thereby furnishing theoretical guidance for enhancing heat transfer within electronic devices.