Distraction osteogenesis (DO) is widely utilized for treating limb length discrepancy, nonunion, bone deformities and defects. This study sought to develop a 4D time‐lapse morphometry method to quantify bone formation and resorption in mouse femur during DO based on image registration of longitudinal in vivo micro‐CT scans. Female C57BL/6 mice (n = 7) underwent osteotomy, followed by 5 days of latency, 10 days of distraction and 35 days of consolidation. The mice were scanned with micro‐CT at Days 5, 15, 25, 35, 45, and 50. Histological sectioning and Movat Pentachrome straining were performed at Day 50. After registration of two consecutive micro‐CT images of the same bone (day x and day y), the spatially‐ and temporally‐linked sequences of formation, resorption and quiescent bones at the distraction gap were identified and bone formation and resorption rates (BFRdayx‐y and BRRdayx‐y) were calculated. The overall percentage error of the registration method was 2.98% ± 0.89% and there was a strong correlation between histologically‐measured bone area fraction and micro‐CT‐determined bone volume fraction at Day 50 (r = 0.89, p < 0.05). The 4D time‐lapse morphometry indicated a rapid bone formation during the first 10 days of the consolidation phase (BFRday15–25 = 0.14 ± 0.05 mm3/day), followed by callus reshaping via equivalent bone formation and resorption rates. The 4D time‐lapse morphometry method developed in this study allows for a continuous quantitative monitoring of the dynamic process of bone formation and resorption following distraction, which may offer a better understanding of the mechanism for mechano‐regulated bone regeneration and aid for development of new treatment strategies of DO.