Dissipative particle dynamics (DPD) is modified by introducing attractive force. Attractive interaction of liquid and solid and micro-scale flow in nano throats is simulated to discuss mechanism of boundary layer. It is found that thermal motion affects velocity significantly in molecular scale while pressure gradient is leading function as greater than molecular scale. However, thermal motion cannot change integral moving direction. As throat radius becomes larger, parabola shape of velocity distribution becomes more and more obvious. Boundary layer thickness is affected by pressure gradient, throat radius and fluid viscosity. As pressure gradient increases and fluid viscosity decreases, boundary layer thickness decreases. As throat radius decreases, boundary layer thickness increases first and then decreases. Boundary layer is essential reason of nonlinear flow behavior and thickness of boundary layer increasing makes nonlinear flow behavior more obvious.