Ankylosing spondylitis (AS) patients whose symptom onset occurs before 16 years of age are termed juvenile-onset ankylosing spondylitis (JAS). Investigations suggested that JAS had worse functional outcome, and abnormality of bone metabolism can appear in early stage of AS. The objectives of this study are to compare changes of serum inflammatory and bone metabolic markers and to explore the relationship between these biomarkers and disease activity in JAS with different HLA-B27 subtypes. Serum matrix metallopeptidase-3 (MMP-3), soluble receptor activator of nuclear factor-κB ligand (sRANKL), and osteoprotegerin (OPG) were detected by ELISA in 56, 62, and 68 JAS patients, respectively, and 32 healthy individuals were as controls. Serum MMP-3 and sRANKL were significantly higher and OPG in JAS was slightly higher than those in controls. There was no significant difference in the level of MMP-3, sRANKL, and OPG among JAS patients with B27 negativity, B2704, B2705, and B*2715, respectively. Serum levels of MMP-3 showed positive correlation with BASDAI and BASFI (Bath Ankylosing Spondylitis Disease Activity Index and Functional Index). Serum level of sRANKL showed positive correlation with MMP-3 and negative correlation with disease duration. The significantly higher sRANKL expression suggested the enhanced osteoclast function and imbalance of RANKL/OPG system in the inflammatory process of JAS patients carrying different B27 subtypes. It should be paid attention to the abnormality of bone metabolism during the treatment of JAS.