A 3D target inversion algorithm based on multi-feature reconstruction was proposed in order to solve the problems of large memory occupation and time-consuming training in deep learning-based three-dimensional inversion methods. Four types of features, horizontal area, center depth, vertical thickness and residual density of the target were extracted by feature decomposition to realize the compression of the three-dimensional model and reduce the memory occupation. The multi-feature reconstruction of inversion network (MRNet) was designed to realize the prediction of the four types of target features by different Decoder, and the four types of features were used to reconstruct the three-dimensional model to realize the inversion of the 3D target. The gradient union was introduced at the input of the network to realize the enhancement of target boundary information. The CA attention mechanism was introduced at the cross-layer connection to realize the differentiation of Decoder’s prediction function and optimize the inversion effect. The simulation results showed that the local relative accuracy of MRNet was improved by more than 30% compared with 3D U-Net, reaching 88.91%, and the training time per round was only 1/13 of 3D U-Net. MRNet was applied to Vinton Salt Mound, and the distribution of caprocks was obtained more accurately, which verified that MRNet had certain generalizability.