The Emeishan large igneous province is located in the southwest of China. At~260 Ma in the late Permian period, it erupted massive continental flood basalts. For such an event, there must be a large-scale underground magmatic system for magma accumulation and migration in the subsurface. After the eruption is over, the underground magmatic system might be filled with mafic magma and becomes a part of the lithosphere. The solidified mafic-ultramafic intrusions, which are usually strongly magnetized, may cause magnetic anomalies. Thus the magnetic method can be used to detect such a system in the earth. In this research, magnetic anomaly grid data is applied to image the deep structure of the Emeishan large igneous province. The magnetic anomalies in this area consist of a series of discrete ones with obvious remanence, implying that the direction of magnetization is inconsistent with that of the current geomagnetic field. Since the classical 3D inversion method is based an assumption that there is only induced magnetization, the inversion result would be inaccurate due to the existence of remanence. Thus, we first transform the magnetic anomalies to magnetic amplitude data, which is less sensitive to the direction of magnetization. Then we use the amplitude data for 3D inversion to obtain the distribution of magnetic anomaly sources within the lithosphere. These underground discrete magnetic sources may indicate the mafic-ultramafic intrusions beneath the Emeishan large igneous province. These intrusions might be formed during underplating or intraplating in the Emeishan large igneous province, which might be magma chambers or magma transport channels filled with mafic magma. After cooling, these mafic-ultramafic intrusions would have produced magnetic anomalies observed now.