To solve the problem of a uneven load for a dual-input counter-rotating transmission system, this research is based on Small Displacement Torsor Jacobian-Torsor theory.Considering the influence of the local parallel chain of a gearbox on the calculation accuracy of the backlash,the processing method of a meshing tooth pair parallel chain is proposed. The probability distribution of the tolerance band of gearbox manufacturing and assembly errors is modeled, the three-dimensional tolerance analysis model of a dual-input counter-rotating gearbox is established, and the Monte Carlo method is used to solve the backlash of the output end. The output backlash is solved with the Monte Carlo method, and the theoretical design backlash is combined with the output backlash to derive the gearbox side clearance range. The gearbox shaft system is analyzed statically, the range of the equal load coefficient is calculated, and the equal load performance optimization method based on the matching relationship between the gear backlash and the elastic shaft torsional stiffness is proposed. The correctness of the three-dimensional tolerance analysis combined with the elastic deflection angle used to optimize the equal load performance of the dual-input counter-rotating transmission system is verified by comparison with the relevant test data.