The invention discloses a wall boundary simulation method in molecular dynamics simulation. The method integrates the advantages of a total reflection method and a random reflection method, can truly reflect the motion state of a particle after colliding with a wall and is also called as a semi-reflection method. The method comprises the following steps of: (1) defining a data structure of the particle in the molecular dynamics simulation; (2) determining the current position A (x0, y0, z0, u0, v0, w0) of the particle in a channel; (3) determining the motion direction of the particle according to the current position of the particle and information of acting force by other particles of the particle, and judging whether the particle can move to other positions beyond the wall boundary in anext step or not according to the current position and the acting force information of the particle; and (4) if the particle moves to a position beyond the wall boundary, reflecting the particle through the wall to a next reflection position B (x, y, z, u, v, w), wherein if the wall exists in the x direction, y is equal to y', z is equal to z', x is equal to 2*x' (which is the coordinate of the wall in the x direction), and the speed direction of the particle is random. In the simulation of the invention, physical conditions of wall constant temperature and wall roughness can be reflected, the position of the reflected particle can be more truly reflected, and the method also can be applied to an irregular nano channel to simplify the calculating method of a velocity vector.