The accurate estimation of axial stresses is a major problem for high-strength bolted connections that needs to be overcome to improve the assembly quality and safety of aviation structures. However, the conventional acoustoelastic effect based on velocity-stress dependence is very weak for short bolts, which leads to large estimation errors. In this article, the effect of axial stress on ultrasonic scattering attenuation is investigated by calculating the change in the energy attenuation coefficient of ultrasonic echoes after applying axial preload. Based on this effect, a stress-dependent attenuation estimation model is developed to measure the bolt axial stress. In addition, the spectrum of the first and second round-trip echoes is divided into several frequency bands to calculate the energy attenuation coefficients, which are used to select the frequency band sensitive to the axial stress changes. Finally, the estimation model between axial stress and energy attenuation coefficients in the sensitive frequency band is established under 20 steps of axial preloads. The experimental results show that the energy attenuation coefficient in the sensitive band corresponds well with axial stress. The average relative error of the predicted axial stress is 6.28%, which is better than that of the conventional acoustoelastic effect method. Therefore, the proposed approach can be used as an effective method to measure the axial stress of short bolts in the assembly of high-strength connections.