The invention discloses a design method of a two-stage cylindrical gear reducer, which comprises the following steps: (1) determining working conditions, (2) determining an objective function and a design variable, and (3) encoding and engineering processing of the design variable, specifically including mapping processing of discrete variables and encoding processing of continuous variables; (4)determining a constraint condition and a fitness function; and (5) substituting the established mathematical model into a discrete shuffled frog leaping algorithm, and outputting an optimization calculation result. According to the design method, manual calculation can be greatly reduced, the basic parameters of the two-stage gear reducer can be automatically calculated and designed only by inputting the basic parameters such as the target type, the working condition and the constraint condition into the program provided by the invention, and the result is more accurate and reliable.