In order to properly simulate bolted joints and make the numerical modes as accurate as possible, this paper is focused on modeling methods for dealing with bolt connection structures composed of two sheets. Six methods are presented to establish the FE models using different element types(8-node brick elements and 4-node shell elements) and different constraints (such as contact interaction and coupling constraint). The models are solved in ABAQUS software and natural frequencies and vibration shapes are obtained. Then, the experiments of bolt fastening structures are performed and FE simulation results are compared with the experimental ones. Moreover, the methods which agree well with the experiments are selected as the FE model of bolted connection. Finally, the element layers in the through-thickness direction are discussed. FE models built in this paper can reflect the real situation of bolted joints and provide significant reference to FE analysis for the complex system connected by bolts.