Main reducer is an important component of helicopter drivetrain, and its quality has a crucial impact on the whole transmission. A design method of main reducer configuration based on graph theory is proposed in this paper, taking coaxial counter rotating helicopter’s gearbox as objective. Firstly, connection laws, boundary conditions and gear units are obtained by concluding existing literatures 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, in order to verify rationality of this method, designing and screening process of 3-stage main gearbox schemes of cylindrical gear configuration is listed.