A new algorithm to extract the velocity caused by the external forces in molecular dynamic simulation of nanoscale flow problems is proposed. The flow velocity, an important component in these type of problems, is usually obtained from the average value in the time space because the accumulation of the thermal velocity will approach zero when the time period is large, but this method is not always suitable, especially when the flow velocity is much smaller than the thermal velocity. Based on the idea of the linear accumulation of the flow velocity, in this study a new algorithm is derived to extract the flow velocity. This algorithm can be used to calculate nanoscale flow problem no matter whether the value of the flow velocity is big or small. Using this new algorithm, the 2-D liquid flow of argon in nanochannels was simulated. The numerical result demonstrates the effectiveness of the new algorithm.