Abstract: Objective The purpose of this study was to locate brackets in digital models by digital integrated modeling, and indirect bonding transfer trays were made by computer-aided design and computer-aided manufacturing, besides, the indirect bonding system was tried for the clinical application. Methods Crowns were scanned by laser, and roots of teeth and jaw bones were rebuilt by three-dimensional CBCT images. Then the three-dimensional CBCT images and laser scanning images were integrated. Three-dimensional digital dental models were built including crwns, roots and jaws. OrthoRx software was used for brackets positioning in integrated models, indirect bonding transfer trays were made, and the transfer trays were used for bonding brackets in clinics. Results Brackets positioned by OrthoRx software were very good in tooth arrangement. Brackets were well transferred into patients’ mouths by indirect bonding transfer trays made by computer-aided manufacturing. The brackets were bonded firmly. Conclusion: OrthoRx software was very good in brackets positioning. It can also present tooth arrangement effect. Individual indirect bonding transfer tray can be made by computer-aided design and computer-aided manufacturing, and it may be useful in clinics.