The tightening process of aero-engine rotor bolt involves a nonlinear bonding stage, which poses challenges in achieving accurate control of the pre-tightening force using the way of torque control. This study proposes a secondary tightening control strategy that offers high precision and adaptability for controlling the bolt pre-tightening force based on the snug point. Firstly, we provide a detailed description of the variable stiffness process during the nonlinear bonding stage of bolt, based on theories related to bolt torque-pretension relationship and bolt deformation coordination relationship. Secondly, we design methods for extracting the snug point and calculating the target rotation angle through the Monte-Carlo simulation model and the linear goodness of fit evaluation mechanism. Thirdly, we experimentally investigate the effectiveness of this secondary tightening strategy using the typical connection section of aero-engine rotor flange bolt as our experimental object. The results indicate that applying this secondary tightening strategy can effectively mitigate uncertainties caused by nonlinear bonding and reduce errors resulting from variations in bolt characteristics and external conditions. Compared to torque control method and torque-angle control method, employing this secondary tightening strategy reduces the standard deviation of pre-tightening force from 1.875 and 1.031 to 0.536, thereby minimizing dispersion in pre-tightening force level. Additionally, it reduces maximum deviation of pre-tightening force from 30.9% and 20.1% to 2.8%, significantly enhancing accuracy in controlling bolt tightening.