Currently, most predictions related to bridge geometry use shallow neural networks, which limit the network’s ability to fit since the input form limits the depth of the neural network. Therefore, this study proposed a new 3D representation of bridge structures. Based on the geometric parameters of the bridge structure, three 4D tensors were formed. This form of representation not only retained all geometric information but also expressed the spatial relationship of the structure. Then, this study constructed the corresponding 3D convolutional neural network and used it to estimate the frequency of the bridge. In addition, this study also developed a traditional shallow neural network for comparison. The application of 3D representation and 3D convolution could effectively reduce the prediction error. The 3D representation presented in this study could be used not only for frequency prediction but also for any prediction problems related to bridge geometry.