To explore the correlation between the ultrasound-detected synovitis in each individual joint at metacarpophalangeal (MCP), proximal interphalangeal (PIP), and metatarsophalangeal (MTP) regions and the clinical disease activity in patients with rheumatoid arthritis (RA). Clinical disease activity was assessed by disease activity score (DAS) based on 28-joint count and erythrocyte sedimentation rate (DAS28-ESR), C-reactive protein (DAS28-CRP), Simplified Disease Activity Index (SDAI), and Clinical Disease Activity Index (CDAI). Gray scale (GS) and power Doppler (PD) synovitis was assessed by ultrasound semi-quantitatively. The correlation between clinical disease activity indices and synovitis score in each joint was assessed using Spearman's rank correlation test. 211 RA patients were included in this study. The whole GS scores of all MCP joints showed the highest correlation with each Clinical Disease Activity Index (r = 0.403-0.452, p < 0.01). Likewise, the whole PD scores of all MCP joints also showed the highest correlation with clinical disease activity (r = 0.332-0.396, p < 0.01). At individual joint level,the highest correlation of GS score with DAS28-ESR (r = 0.411, p < 0.01), DAS28-CRP (r = 0.459, p < 0.01), and SDAI (r = 0.444, p < 0.01) was observed in MCP3 joint while with CDAI (r = 0.421, p < 0.01) in MCP2 joint. The highest correlation of PD score with DAS28-ESR (r = 0.353, p < 0.01), DAS28-CRP (r = 0.399, p < 0.01), CDAI (r = 0.368, p < 0.01), and SDAI (r = 0.377, p < 0.01) was observed in MCP5 joint. The ultrasound-detected synovitis at MCP joints, especially MCP2, MCP3, and MCP5 joints, was best correlated with clinical disease activity in most RA cases, in contrast to PIP and MTP joints. Key Points • The correlation of ultrasound-detected synovitis in each individual joint with the clinical disease activity in RA patients is diverse among joint regions. MCP joints showed the best, in contrast to PIP and MTP joints.