A negative inversion structure cause analysis method and system, an electronic device, and a storage medium, the method comprising: constructing a geological generation model of a negative inversion structure, the geological generation model comprising two stratums separated by a pre-stored slab fault; the geological generation model is correspondingly controlled sequentially according to an extrusion stage and an extension inversion stage, and the extension angles of the two stratums in the extension inversion stage can be adjusted; recording geometric and kinematic characteristics of the geological generation model at different extension angles in each stage; and acquiring geographic features of a to-be-analyzed region, matching the geographic features with the geometric and kinematic features, judging whether the to-be-analyzed region belongs to a negative inversion structure, and if so, acquiring an extension angle of the to-be-analyzed region in an extension inversion stage. By means of the method, cause analysis can be conducted on the negative reversal basin in the river-side depression, the tectonic deposition appearances of the negative reversal basin in different periods are analyzed, and supplementary suggestions are provided for geological exploration of the basin.