Micro-slip friction often occurs at the contact interface of bolted joint structures under long-term oscillating loads. Frequent micro-slip may cause the bolt preload to decrease or even bolt loosening. Acoustic emission (AE) is a phenomenon happening during the micro-slip friction and contains abundant physical information. Developing a micro-slip friction AE model can link AE signal characteristics with tribological conditions, and further guide the application of AE technique into the bolt looseness detection. Therefore, this paper establishes a theoretical micro-slip AE model for bolted joint structures. The main steps of establishing the theoretical AE model are: Firstly, the elastic energy stored in a single asperity during the stick-slip friction is studied. Secondly, the overall elastic strain energy is obtained using the statistical analysis method and the characteristics of micro-slip are considered based on the Mindlin solution. Finally, the strain energy release rate and AE root means square (RMS) are calculated considering the additional sliding velocity and AE signal converting ratio. Reciprocating micro-slip experiments of a bolted joint structure are carried out to verify the accuracy of the proposed AE model. The tangential behavior and the normal behavior of the bolted joint structure are changed respectively. The results show that the proposed theoretical model can accurately describe the variation trend of AE Vrms with operating parameters. And the theoretical AE Vrms calculated by the proposed AE model are more coincident with the experimental results compared with the gross-slip AE model. In summary, this paper novelly proposes a micro-slip AE model based on the Mindlin contact solution and considers the relationship between surface separation and bolt preload, which lays the foundation for applying AE technique in the early stage of bolt looseness monitoring.