The invention relates to a freeze-dried protein renaturation method based on a natural phenomenon that solute is naturally separated from solvent in the solution freezing process. The solubility of solute salt in a solution is influenced by temperature, denaturation salt (urea, guanidine hydrochloride, and the like) is gradually crystallized and separated from the solution because the solubility of the denaturation salt lowers at a low temperature, and two vital denaturation factors, namely molecular heat movement and the denaturation salt concentration of the solution, are reduced. The crystallization speed can be controlled by the temperature drop speed so as to establish a wonderful condition for protein renaturation, namely the low temperature as well as a smooth downward gradient of the denaturation salt concentration. Meanwhile, a renaturation solution is aided with antifreezing agents (DMSO, fucose, glucose, and the like) with a certain concentration, renaturation activators (cyclodextrin, glycin, molecular chaperones, and the like), reductant-oxidant, buffer salts, and the like for preventing freezing damage to the protein activity and improving the renaturation rate. The frozen dry protein is dried by a freeze drier to obtain solid particles which are suitably vibrated to break by utilizing the difference between the denaturation salt and dry protein powder in the crystallization proportion and the crystallization form and separated by adopting the methods of pneumatic separation, sieving, electrostatic adherence and the like to obtain target protein.