AbstractBased on the geomagnetic field model (NGDC‐720) established by the U.S. National Geophysical Data Center, the spatial variations of crustal magnetic anomalies in the Yunnan region were studied, including the distribution of magnetic anomalies and their gradients, attenuation of magnetic anomalies with altitude, and the contributions of components with different wavelengths to overall magnetic anomalies. The magnetic anomalies were compared with other geophysical data such as gravity anomalies, terrestrial heat flow, and seismic activities to reveal similarities and differences, and the relationship between crustal magnetic anomalies and geological structure was studied. The research results show that the magnetic anomalies are relatively weak in the Sanjiang (Three Rivers) and western Yunnan orogenic belts to the west of the Lijiang‐Xiaojinhe and Red River fault zones, and relatively strong in the rhombic block. The crustal magnetic anomalies in the study region were mainly generated by the shallow magnetic bodies superposed on the background of weak magnetism basement. The satellite magnetic anomalies show that the middle Yunnan depression area has clear dipole field characteristics. The positive and negative magnetic anomaly zones distributed along the Red River fault zone have consistent strikes with that of the faults. The Lijiang‐Xiaojinhe fault, the Red River fault, the Kangding‐Yiliang‐Shuicheng fault and the Mile‐Shizong‐Shuicheng fault zones surrounding the rhombic block are transition belts between strong and weak magnetic anomalies. The places with active seismicity and the areas with high terrestrial heat flow values have negative or relatively weak crustal magnetic anomalies.