An automated orthodontic bracket positioning system including a computer system for constructing the digital 3D dental model, a bite record device for acquiring the patient's intra-oral coordinate record, and an automatic bracket positioning device for bonding orthodontic brackets on the patient's tooth surfaces or surfaces of dental cast. The computer system estimates a predicted position of each orthodontic bracket on patient's tooth surface or a surface of the gypsum dental cast by using the digital 3D dental model to control the automatic bracket positioning device to position the brackets on the patient's tooth surface or surfaces of the dental cast according to the predicted position.