The Nihe iron deposit is a typical porphyrite type iron deposit with large burial depth,small amplitude of gravity and magnetic anomalies generated at the surface in Anhui Province. The authors selected the Nihe iron deposit to carry out gravity and magnetic inversion experiment based on known information constraint, in order to evaluate the application effect of gravity and magnetic data fine-grained and three-dimensional inversion in magnetite deep exploration: First of all, through the model test, the authors compared the three-dimensional inversion results with different known information constraints, and then extracted the residual gravity and magnetic anomalies of the Nihe iron deposit through the targeted field separation method. Then, the authors transformed the known surface geological information into physical information, and built a remnant density and magnetic susceptibility reference model to constrain gravity and magnetic three-dimensional inversion. Based on the three-dimensional distribution model of inversion density and magnetic susceptibility body, the authors confirmed the three-dimensional spatial shape of the Nihe iron orebody, and found that the result is basically consistent with geological exploration results. According to the results, the reliability of the inversion results based on the known information constrained gravity and magnetic three-dimensional inversion could be improved. For magnetite with high magnetic and high density, this method is an effective method to find and characterize deep magnetite orebody.