To investigate the effect of assembly gap and shim on single-lap multi-bolt composite joint stiffness, an analytical model based on the spring-mass method was proposed, which converted the multi-bolt joints into individual single-bolt joint based on premise that there are no overlap regions of the highly stressed portions for adjacent holes. The proposed model considers the conical and spherical stress envelope and gradual elimination phenomenon of the bolt-hole clearances for multi-bolt joints. Meantime, an effective-to-equivalent gap area method was proposed to calculate the joint stiffness for situations with arbitrary assembly gap shape. Both experiment and finite element method for three-bolt joints were used to validate the proposed model with different situations of assembly gap and/or shim. The relative error of the shear stiffness between the analytical model and experiment is 0.31%, while that of the bolt stiffness is 19.8%. After that, four interested situations with different assembly gap and/or shims were discussed, and the maximum relative error of the shear stiffness between the analytical model and the finite element model is17.0%, while that of the bolt stiffness is 15.8%. Taking into account the complexity of composite material and that of assembly gap and gap shimming, the proposed analytical model is effective to predict the stiffness of the single-lap multi-bolt composite joints subjected to single-shear loading.