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The correlation analysis between gear modification and vibration characteristics of transmission system was difficult to quantify; a novel small sample vibration of gearbox prediction method based on grey system theory and bootstrap theory was presented. The method characterized vibration base feature of tooth modification gearbox by developing dynamic uncertainty, estimated true value, and systematic error measure, and these parameters could indirectly dynamically evaluate the effect of tooth modification. The method can evaluate the vibration signal of gearbox with installation of no tooth modification gear and topological modification gear, respectively, considering that 100% reliability is the constraints condition and minimum average uncertainty is the target value. Computer simulation and experiment results showed that vibration amplitude of gearbox was decreased partly due to topological tooth modification, and each value of average dynamic uncertainty, mean true value, and systematic error measure was smaller than the no tooth modification value. The study provided an important guide for tooth modification, dynamic performance optimization.