The invention provides an aircraft surface defect scale controlling method capable of reducing the influence on the flow transition. The aircraft surface defect scale controlling method capable of reducing the influence on the flow transition comprises the steps that first, a theoretical analysis method or a ground test method is used for performing a flow transition study on an aircraft, and a constraint range of the surface defect scale meeting the requirement that the boundary layer transition is not affected is obtained; then the joint simulation analysis of aerodynamic heating, a structural temperature field and a deformation field is carried out on the section where the defect is generated, and the thermal deformation data of each section where the defect is generated during the flight is extracted from the structural deformation calculation result; the strategy of initial defect scale offsetting the thermal deformation is adopted, and based on the constraint range and thermal deformation data, the initial defect scale to be processed is designed to ensure that the actual defect scale meets the constraint range during the flight. The aircraft surface defect scale can be reasonably and effectively controlled, the possibility of inducing surface transition in advance is reduced, and the reliable operation of an aircraft thermal protection system is ensured.