Main reducer is an important component of helicopter drivetrain, and its quality has a crucial impact on the whole transmission. In this paper, taking coaxial counter rotating helicopter’s gearbox as objective, a design method of main reducer configuration based on graph theory is proposed. Firstly, connection laws, boundary conditions and gear units are obtained by review of existing literature of the reducer. Then, automatic generation of adjacency matrix corresponding to main reducer is realized before transforming adjacency matrix to model of graph theory. After setting up rules and screening schemes to yield feasible solution set of the reducer, an optimization procedure, which aims at screening gear weight of feasible solutions and obtaining the solution of the lightest gear weight, is built by SQP (sequential quadratic programming algorithm) method based on gear strength constraints. Finally, to verify the rationality of this method, the designing and screening processes of 3-stage main gearbox schemes of cylindrical gear configuration are listed.