The present disclosure illustrates an automated orthodontic bracket positioning system. This system includes a computer system for constructing the digital 3D dental model, a bite record device for acquiring the patients intra-oral coordinate record, and an automatic bracket positioning device for bonding orthodontic brackets on the patients tooth surfaces or surfaces of dental cast. The computer system estimates a predicted position of each orthodontic bracket on patients tooth surface or a surface of the gypsum dental cast by using the digital 3D dental model. The computer system receives and utilizes the intra-oral coordinate record to calibrate the digital 3D dental model and ensure that the digital 3D dental model match with the patients practical condition, so that the predicted position can accurately match to the patients tooth surface. The computer system controls the automatic bracket positioning device to position the brackets on the patients tooth surface or surfaces of the dental cast according to the predicted position.