ABSTRACT: (1) Background: Continuing to observe the grafted bone mineral density (BMD) is essential to ensure the success of alveolar bone grafting (ABG) in patients with cleft lip and palate. This study elaborates on three methods that can be used to evaluate the progressive BMD. (2) Methods: Forty patients with unilateral or bilateral clefts receiving ABG were enrolled. Cone beam computed tomography (CBCT) scans were taken at 6 months (T1) and 2 years (T2) postoperatively. In CBCT, measurements were obtained on three different planes using the circle located 1 mm from the adjacent teeth (Method A), the largest circle within the defect (Method B), or the central circle with a diameter of 2 mm (Method C). The BMD was the average density of the three planes and was adjusted by pogonion density. Bland-Altman plots were used to evaluate the agreement of each method. Inter-rater reliability was confirmed by the intraclass correlation coefficient (ICC). (3) Results: For Method A, B, and C, the mean-adjusted BMD (BMD/pogonion density, BMDa) was 17.44%, 17.88%, and 17.69%, respectively, at T1 (p = 0.495), and 22.51%, 22.87%, and 22.74%, respectively, at T2 (p = 0.690); the density enhancement rates were 40.54%, 38.92%, and 43.15% (p = 0.382). Significant differences between the BMDa at T1 and T2 were observed (p < 0.001, <0.001, and 0.001, for Method A, B, and C, respectively). The volume of the grafted tissue remained stable during T1 and T2, and no significant correlation between density enhancement rate and volume loss was observed. (4) Conclusions: A significant increase in the BMD of grafted tissue was observed in the 2-year postoperative follow-up. The three methods for measuring BMDa via CBCT can be applied in post-ABG evaluations.