Mandibular deviation affects the biomechanical environment of the temporomandibular joint (TMJ) and causes thinning of cartilage on the deviated side. We aimed to evaluate, using a rat model, the effect of mandibular functional deviation on the TMJ in relation to the functional roles of integrin β family members. The effects of experimental functional deviation on the TMJ of 6-week-old Sprague-Dawley female rats, randomly assigned to control (n = 42) and experimental groups (n = 42), were evaluated at 3 days and 1, 2, 4, and 8 weeks by histological staining, immunofluorescence, real-time quantitative polymerase chain reaction, and micro-computed tomography. The results showed that the experimental functional shift changed the shape of condyles, thinned the cartilage, and increased the proportion of the hypertrophic layer on the deviated sides of condyles. In addition, the extracellular matrix of the condyle cartilage exhibited degradation at 1 week and subchondral trabecular bone was lost at 4 and 8 weeks. Osteoarthritis (OA)-like changes occurred in the left and right condyles of rats in the experimental group and were aggravated over time. Integrin β family expression, especially integrin β , was altered from week 1, possibly related to the OA-like changes. These data may provide insight into the onset of TMJ OA.