Torque control method is commonly used when tightening bolted joints because of its easy operation. However, the method involves an essential problem of fairly large scatter in bolt preloads. It has been reported that even if the same torque is applied, bolt preloads show a considerable scatter, e.g., ranging from 25% to 35%. A scatter in coefficients of friction on nut bearing surface and thread pressure flank is a primary source of bolt preload scatter. Meanwhile, the effect of Equivalent Friction Diameter at the bearing surfaces of nut and bolt head cannot be ignored. The scatter in Equivalent Friction Diameter is caused by imperfect geometry, i.e., the flatness deviation at the bearing surfaces. In this paper, the magnitudes of Equivalent Friction Diameter are quantitatively evaluated by FEA, using the experimental data of flatness deviation measured for a number of commercial nuts and bolts. It is shown that the bolt preload is likely to be scattered by as much as plus minus 10% of the target value, owing to the flatness deviation. Based on the comprehensive calculations by considering the imperfect geometry, a strategy to effectively suppress the bolt preload scatter is proposed.