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The Sichuan Basin magnetic anomaly is the most striking regional aeromagnetic anomaly in South China. It is characterized by a continuous large-scale linear magnetic anomaly and contains long-wavelength constituents which could still be detected on satellites. However, Sichuan Basin is covered by 4 to 10 km thick non-magnetic sedimentary layers from Neoproterozoic to Cenozoic, which conceals the magnetic sources in the Precambrian basement and makes it difficult to explore the geological origin of the Sichuan Basin magnetic anomaly. In this study, we applied 3D inversion to the magnetic data, and then compared our inverted susceptibility model with geological maps. We found that the spatial distribution of the Sichuan Basin magnetic anomaly controls the range of the rigid basement beneath Sichuan Basin and it is surrounded by the widespread Neoproterozoic magmatic complexes. Based on our analysis, we proposed that the geological origin of the Sichuan Basin magnetic anomaly might be related to the craton-scale Neoproterozoic magmatic event, which has played an important role in the stabilization of the basement and the evolution of the deep crust in Sichuan Basin.