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As the integrity of micro electronic devices improves, the heat power of chips is getting higher and higher. Micro-channel heat sink has been got more and more concerns for its better cooling performance. A lot of investigations about micro-channel coolers have been undertaken in the past years. As a result of the impact of micro-pump power, the traditional silicon micro-channel heat sink cooling has shown its weakness. Considering the orders of magnitude of the thermal conductivity of carbon nanotubes (CNTs) are higher than the metal material, therefore, using carbon nanotube fin to replace silicon fin will improve the micro-cooler performance significantly. This paper carried out the molecular dynamics simulation of water besides CNTs in CNTs micro-channel cooler. The motion model of CNTs and water molecule was established. The movements of water molecule at the interface of the CNTs with the different inlet velocities and the density were analysed. The study found that the number of water molecules close to the CNTs was the minimum and that of the second closing layer of water molecules was more because the repulsion force between the CNTs and water molecules and the attraction effect between the CNTs and less water molecules, some water molecules moved into the CNTs. Simulation results showed that the water molecules at the surface of the CNTs had the velocity slip phenomenon.