The objective of this study was to assess the possibility of developing a clinical minimally invasive and standardized method to evaluate the relationship between the microstructure of the jaw bone and systemic bone turnover. For this purpose, we performed standardized bone biopsy of the alveolar bone, and compared the 3D bone microstructure using micro-computed tomography (micro-CT) with bone mineral density (BMD) of the lumbar spine and biochemical markers of bone turnover. We evaluated a total of 9 samples taken from 6 patients by standardized biopsy using a trephine bur. BMD was evaluated using dual energy X-ray absorptiometry (DXA). Regarding the biochemical markers of bone turnover, serum bone-specific alkaline phosphatase (BAP) and serum osteocalcin (OC) were used as bone formation markers, and urinary cross-linked N-telopeptides of type I collagen (NTx) and urinary deoxypyridinoline (DPD) were selected as bone resorption markers. We scanned micro-CT images of these samples. Bone volume fraction (BV/TV), trabecular thickness (Tb.Th), trabecular number (Tb.N), trabecular spacing (Tb.Spac), fractal dimension, trabecular bone pattern factor (TBPf) and node-strut (Nd.Nd/TV, TSL/TV) were measured. Regarding the correlations between the parameters of bone microstructures, TB/TV, Tb.N, fractal dimension, and node-strut seemed to be positively correlated and Tb.Spac and TBPf seemed to be negatively correlated with each other, but Tb.Th seemed to have a low correlation with other parameters. OC and/or BAP showed a significantly high correlation with many structural parameters (p<0.05%). In conclusion, some microstructural parameters may change according to the systemic bone turnover.