The invention relates to an encryption method and device of a power system control protection program and a storage medium. The encryption method comprises the following steps: analyzing information of all modules, variables and connecting lines in a program according to the content of the control protection program, summarizing to form a data chain with a logical operation function, adding attribute setting information of the modules and the variables, finally combining to form a character string containing specific data information, and finally performing encryption calculation. The encryption method can ensure that the control protection program downloaded to the device on the engineering site is accurate.