Murine models for rheumatoid arthritis (RA) research can provide important insights for understanding RA pathogenesis and evaluating the efficacy of novel treatments. However, simultaneously imaging both murine articular cartilage and subchondral bone using conventional techniques is challenging because of low spatial resolution and poor soft tissue contrast. X-ray phase-contrast imaging (XPCI) is a new technique that offers high spatial resolution for the visualisation of cartilage and skeletal tissues. The purpose of this study was to utilise XPCI to observe articular cartilage and subchondral bone in a collagen-induced arthritis (CIA) murine model and quantitatively assess changes in the joint microstructure. XPCI was performed on the two treatment groups (the control group and CIA group, n = 9 per group) to monitor the progression of damage to the femur from the knee joint in a longitudinal study (at 0, 4 and 8 weeks after primary injection). For quantitative assessment, morphologic parameters were measured in three-dimensional (3D) images using appropriate image analysis software. Our results showed that the average femoral cartilage volume, surface area and thickness were significantly decreased (P<0.05) in the CIA group compared to the control group. Meanwhile, these decreases were accompanied by obvious destruction of the surface of subchondral bone and a loss of trabecular bone in the CIA group. This study confirms that XPCI technology has the ability to qualitatively and quantitatively evaluate microstructural changes in mouse joints. This technique has the potential to become a routine analysis method for accurately monitoring joint damage and comprehensively assessing treatment efficacy.