The operational safety and stability of wind turbines are highly determined by the characteristics of main bearings, which are influenced by the axial clearance. In this paper, for the arrangement type of double-supported tapered roller bearings on the wind turbine main shaft, the actual clearance distribution assumption is established, and a new method of calculating the internal load distribution taking into account the axial clearance is proposed. Firstly, the mathematical relationship between the clearance of tapered roller bearings and ring displacement, contact deformation, and load interval is described. Secondly, the load components of main bearings are calculated by force balance equation and load-displacement condition. Finally, a mathematical model of main bearings including axial clearance is established, and it is numerically solved to obtain the internal load distribution of the bearings. The calculation results of a large megawatt wind turbine example show that: the axial load of both main bearings is negatively correlated with the sum of axial clearances; the number of loaded rolling elements is negatively correlated with the sum of axial clearances; and there exists an optimal value of the sum of axial clearances for main bearings to reach the optimal load carrying state.