The accurate measurement of the axial stress of the core engine rotor bolts is of great significance for improving the assembly quality and safety of aeroengines. To solve the problem that the thickness change of the coupling layer affects the measurement accuracy in ultrasonic measurement of axial stress, a measurement method based on time difference compensation of the thickness change of the coupling layer is proposed in this article. Based on the principle that different loads applied to the ultrasonic transducer will cause the thickness of the coupling layer to change, which leads to changes in the amplitude and propagation time of the ultrasonic echo signal, the principle of time difference compensation for changes in the thickness of the coupling layer is proposed. Based on this principle, the propagation time difference caused by the thickness change of the coupling layer is compensated, thereby improving the measurement accuracy of the propagation time difference caused by the stress and reducing the measurement error of the axial stress. The experimental results show that the average errors of the axial stress measurement model based on the time difference compensation of the thickness change of the coupling layer and the conventional axial stress measurement model are 1.048 and 1.723 MPa, respectively. Therefore, the time difference compensation for the thickness change of the coupling layer can effectively reduce the measurement error of the axial stress. This study provides a promising method for the accurate measurement of the axial stress of aeroengine bolts.