A three-dimensional electrical resistivity tomography method and system belonging to the field of geological geophysical prospecting, the method including the steps of prospecting a region containing a geological anomaly with at least two prospecting modes respectively to acquire two-dimensional resistivity data of a corresponding detection plane; unifying coordinate systems of resistivity data points acquired in all prospecting modes, and extracting data points with the same coordinates; carrying out data fusion on extracted resistivity data at the same position by utilizing a principal component analysis method; and carrying out three-dimensional coordinate conversion on resistivity data acquired after fusion to form a three-dimensional model.