The invention provides a data processing method and a medical scanning system. The method includes the following steps that panoramic data, acquired at least twice by panoramic photography equipment, of a scanned object is obtained, and the panoramic data acquired at least twice corresponds to at least two scanning stages of the scanned object respectively; according to the panoramic data acquired at least twice, registration is conducted, placement difference information corresponding to the scanned object between the panoramic data acquired at least twice is obtained; according to the placement difference information, scanning data obtained by scanning the scanned object is corrected. The method and the system achieve the effective control over the scanning process.