Micro/nanoscale thermofluidic transport is remarkably different from the conventional flow , due to its much smaller spatial and temporal scales. From the perspective of convectional theory, the smaller size of the device is, the higher the efficiency of convective heat transfer can be achieved. In other words, micro/nanoscale heat transfer brought up a promising opportunity to dramatically improve efficiency of thermal control if the scale of a device is miniaturized significantly. This explains why micro/nanoscale heat transfer became such an attractive research topic across the entire engineering field in the past two decades. In order to have a better understanding of the mechanism of convective heat transfer in micro/nanoscale, a number of researches have already been conducted in the past years. With the purpose of result benchmark, study from a simple fluid flow problem that have analytical solution available is always a better choice. One of these fundamental fluid flow problems is Couette type flow where the fluid flows at the space between two parallel plates with one plate moving and the other stationary . In fact, a variety of work deal with Couette type heat transfer problem can be found in the literature [2-9]. It is well known that the analytical solution for Couette flow problem can be easily obtained; however, it is also true that continuum assumption break down when the size of interested domain is approaching micro/nanoscale (depends on Knudsen number). MD simulation, which is able to describe the physical process from atomic level, is emerging as a powerful tool to provide detailed information on thermal properties at high shear rates or other extreme conditions for fluid flow problems in the micro/nanoscale. In fact, several similar simulation works have been reported to study these particular phenomena caused by the size effect. Jabbarzadeh et al.  investigated the boundary condition of the flow in molecularly thin liquid films of alkanes with roughness modeled by a sinusoidal wall using MD simulation. Soong et al.  investigated a Couette flow to study the effects of wall crystal–fluid interactions in nanochannels by MD simulation. Slip characteristics on absorbing surfaces under different conditions were explored by using MD simulation of thin films of hexadecane . Khare et al.  studied the thermal resistance of a model solid–liquid interface using MD. It was found that the interfacial thermal resistance increased with the presence of velocity slip while it was not affected by the mass flow in the absence of the velocity slip. Nagayama and Cheng  carried out MD simulations to study the effect of the interface wettability on the pressure driven flow in a nanochannel. The results showed that the temperature and pressure profiles were distributed nonuniformly due to the effect of interface wettability. Among these similar works, the temperature and velocity for fluid film were controlled separately, which conflict with the fact that both momentum and temperature are controlled by the same molecular transport. Meanwhile, few researchers paid attention on estimation of heat transfer coefficient between fluid and solid wall during the fluid flow.