The present invention relates to an emulation method for simplifying linear flexible macromolecular dynamic. By starting with pharmacodynamic group of pharmaceutical molecule or active site of receptor a schematic model of molecular simplified linear portion with 'ball-virtual spring' structure is created. In the model one end of linear portion of fixed on the molecular mother body, and the linear portion is formed from ball and virtual spring which are alternatively connected, in which the ball is an equivalent atom obtained by making mass of heavy atom and light atom connected with it and rotatory inertia be equivalent on an atom, and the virtual springconnected between equivalent atoms simultaneously has characteristics of spring and rod. According to noncovalent bond potential between atoms in the 'ball-virtual spring' model and acting force between atoms an equation of motion of plexible linear molecular model with transverse expansion, axial twisting vibration and linear oscillation an be created so as to simulate the existed form of linear bio-receptor macromolecular low-energy conformation. Said invention can be used for computer-aided pharmaceutical design.