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The three-dimensional magnetic structure of the Yangtze River basin was determined using three-dimensional oblique magnetization regularization inversion with high-precision total magnetic anomalies. Large magnetic bodies of varying thickness exist under the Yangtze River basin. The thickness variation of the magnetic layers, which is thin in the north and thick in the south, reflects the crust’s deep tectonic framework. The results do not suggest that the Tan–Lu fault extends southward through the Yangtze River basin. Furthermore, these findings support that the southeast subduction mode of the North China Block in relation to the Yangtze block and the Jiangnan orogenic belt is related to underplating.