The mood disorders have been recognized as common comorbidities of rheumatoid arthritis (RA), however unknown in patients with different RA courses. Therefore, we aimed to investigate the status of mood disorders in early RA and non-early RA patients and further identify the associated factors for mood disorders. Self-rating anxiety scale (SAS) and self-rating depression scale (SDS) were assessed in all enrolled RA patients. Besides clinical assessments, power Doppler and greyscale (GS) ultrasound of 28 joints was performed. The frequency of mood disorders was compared between early RA and non-early RA patients. Multivariate regression was used to identify the associated factors for mood disorders. Tow hundred one RA patients were enrolled, with 76 early RA (disease duration ≤ 2years) and 125 non-early RA (disease duration > 2years). Mood disorders (depression and/or anxiety) were found in 42 (20.9%) patients. Depression was more frequently observed in early RA than non-early RA patients (26.3% vs. 14.4%, P = 0.036). A similar trend for anxiety was also observed in early RA compared to non-early RA patients, although the difference was insignificant (13.2% vs. 5.6%, P = 0.062). Disease duration (OR = 0.991, 95% CI 0.985-0.998, P = 0.009), health assessment questionnaire disability index (HAQ-DI) (OR = 1.045, 95% CI 1.005-1.086, P = 0.029) and GS synovitis score (OR = 1.065, 95% CI 1.017-1.115, P = 0.007) were identified as factors associated with depression. Disease duration (OR = 0.981, 95% CI 0.967-0.995, P = 0.009), HAQ-DI (OR = 1.071, 95% CI 1.013-1.133, P = 0.017) and GS synovitis score (OR = 1.072, 95% CI 1.012-1.136, P = 0.019) were identified to be associated with anxiety. Depression and anxiety were almost doubled in frequency in early RA than in long-standing RA patients. RA patients with short disease duration, high HAQ-DI and GS score were more likely to be in depression and anxiety. Key Points • Mood disorders were more frequent in early RA than non-early RA patients. • More attention to psychological status is needed in RA patients. • RA patients with short disease duration, poor physical function and severe synovitis were more likely to have depression and/or anxiety.