The purpose of this study was to observe the changes in bone-specific alkaline phosphatase (B-ALP) and tartrate-resistant acid phosphatase-5b (TRAP-5b) in a patient diagnosed with short root anomaly (SRA). The detailed clinical data and history of related clinical symptoms of the SRA patient were retrieved. Oral examination showed that the shape and color of the tooth crown were normal. Tooth 11 and 12 were missing, and the mobility degree of other teeth was II-III. Panoramic radiograph examination showed that the root length only reached the neck of the tooth. Laboratory results showed that blood spectrum, chromosome and trace elements were normal. Endocrinological evaluation indicated that hormone levels were within normal limits; however, both B-ALP and TRAP-5b were higher than the normal range. The present case shows that SRA may be related to an imbalance in osteoblast/osteoclast metabolism, which provides a new direction for the etiological research of this disease.