Trans-sutural distraction osteogenesis (TSDO) promotes midface growth in growing cleft lip and palate (CLP) patients with midfacial hypoplasia. The superficial skeletal changes after therapy revealed rotation advancement of the midfacial skeleton associated with differential displacement in each segment, but reports rarely focus on the changes of internal structures, including circummaxillary sutures, the maxillary tuberosity and the maxillary sinus, which may play a crucial role during this process. This study evaluated the computed tomographic (CT) images of 26 growing CLP patients who received bone-borne TSDO therapy. The results revealed that the most prominent new bone formation occurred in the pterygomaxillary suture and pushed the P-point forward. The maxillary first molar exhibited significantly greater advancement compared with the P-point due to the growth of the maxillary tuberosity. The contribution ratio values of the advancement of the maxillary tuberosity and P-point to the maxillary first molar were 26% and 74%, respectively, in UCLP and 25% and 75%, respectively, in BCLP. Furthermore, the maxillary sinus volume was also significantly increased. In conclusion, midface growth with bone-borne TSDO therapy depends on both secondary displacement promoted by sutural bone formation mainly in the pterygomaxillary suture and primary displacement by growth of the maxillary tuberosity and maxillary sinus volume.