Axial spondyloarthritis (axSpA) increases the risk of osteoporosis and vertebral fractures. Bone mineral density (BMD) measured by dual X-ray absorptiometry (DXA) has limitations in axSpA patients. Trabecular bone score (TBS) indirectly assesses bone microarchitecture and can be used to predict fracture risk. However, few studies have investigated the role of TBS in axSpA patients. The objective of this study were to compare TBS between axSpA patients and 1:1 sex- and age-matched healthy volunteers and determine factors associated with low TBS in axSpA patients. A cross-sectional study was conducted in two tertiary-care hospitals. A total of 137 axSpA patients and healthy volunteers were enrolled. Demographics, disease characteristics, and risk factors for osteoporosis were recorded. TBS, BMD at the lumbar spine, hip, and vertebral fractures were assessed by DXA. Low TBS was defined as a TBS value < 1.230. Factors associated with low TBS were examined by logistic regression. Most patients were male (75.9%) and tested positive for HLA-B27 (88.3%). The mean (SD) age was 42.8 (12.0) years. The mean (SD) of TBS in the axSpA patients was lower than those in the healthy volunteers [1.402 (0.107) vs 1.440 (0.086), respectively; p = 0.002]. The mean (SD) of lumbar BMD in the axSpA patients was higher than in healthy volunteers [1.186 (0.212) vs 1.087 (0.124), p < 0.001], whereas the mean (SD) of femoral neck BMD in the axSpA group was lower than that in the healthy volunteers [0.867 (0.136) vs 0.904 (0.155), p = 0.038]. Disease severity as indicated by sacroiliac joint fusion and a high ASDAS score were associated with low TBS with the odds ratios (95% confidence interval) of 11.8 (1.2–115.4) and 5.2 (1.6–16.9), respectively. In conclusion, axSpA patients had a higher prevalence of low TBS than healthy volunteers. Sacroiliac joint fusion and a high ASDAS score were associated with low TBS.