(1) Background: Following the grafted bone mineral density (BMD) is essential to ensure the suc-cess of alveolar bone grafting (ABG) in patients with cleft lip and palate. The study elaborated conducting three methods to evaluate the progressive BMD. (2) Methods: Forty patients with uni-lateral 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 2-mm diameter (Method C). BMD was the average density of the three planes and was calibrated by pogonion density. Bland–Altman plots were used to evaluate the agreement of each method. Inter-rater re-liability was confirmed by the intraclass correlation coefficient (ICC). (3) Results: For Methods A, B, and C, the mean calibrated BMD (BMD/pogonion density, BMDc) 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 BMDc at T1 and T2 were observed (p < 0.001, < 0.001, and 0.001, for Methods A, B, and C, respectively). Volume of the grafted 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 post-operative follow-up. The three methods for measuring BMDc on CBCT can be applied in post-ABG evaluations.