Spondyloarthritis encompasses conditions such as ankylosing spondylitis (AS) and psoriatic arthritis (PsA). Advanced axial spondyloarthritis causes significant spinal fusion, affecting daily activities. Recent therapeutic agents have enhanced the control of inflammation, yet they do not consistently stop the axial progression. This study aimed to identify factors influencing the progression of axial lesions over a two-year period in Japanese patients with axial spondyloarthritis. This retrospective and cross-sectional study included 47 axial spondyloarthritis patients. Spinal lesions were assessed using the modified Stoke Ankylosing Spondylitis Spine Score (mSASSS). Patients were categorized into progressive and non-progressive groups based on changes in their mSASSS scores. Various clinical parameters were analyzed for correlation with ankylosis progression. The study found no significant correlation between ankylosis progression and traditional factors, including the level of inflammation or the use of biologics. However, modified Health Assessment Questionnaire (mHAQ) scores were associated with disease progression. The baseline mSASSS was another significant factor, underscoring the importance of early detection and management. This study showed that patient-reported outcomes and baseline mSASSS scores are crucial for assessing axial spondyloarthritis progression. This underscores the need for a comprehensive treatment strategy that addresses both clinical indicators and patient-reported outcomes.