Obtaining the stiffness variation characteristics of a bolted joint during service is essential for predicting the response of an entire structure. In this study, we propose a relationship between the macro deviation, microtopography of the bearing surface, and hysteretic characteristics of a bolted joint. We first analyze the stiffness variation caused by the hysteretic characteristics during the tightening and service processes. Next, we investigate the influence of non-parallel bearing surfaces and displacement loads on pressure distribution and stiffness, both at macro and micro scales, using Finite Element Modeling (FEM) and experiments. Finally, we compare data from a hysteresis behavior test of a single-bolt lap beam with the FEM simulation results. The comparison demonstrates that macro deviations in the bearing surface alter the preload after assembly, while the bearing surface experiences dynamic changes in pressure due to microtopography and cyclic displacement loads. Consequently, this leads to irregular dynamic changes in joint stiffness during the service process, significantly affecting the dynamic/static response of the bolted assembly structure.