Rheumatoid arthritis (RA) is an inflammatory autoimmune disease triggered by antigenic peptides with environmental and genetic risk factors. It has been shown that antigen-specific targeting could be a promising therapeutical strategy for RA by restoring immune tolerance to self-antigens without compromising normal immunity. Citrullination of antigens enhances antigenic properties and induces autoimmune responses. Here, we showed that citrullinated antigenic (citAg) vaccine ameliorated collagen-induced arthritis (CIA) with decreased T-helper 1 (Th1) and Th17 cells, downregulated proinflammatory cytokines including interlukin-6 and tumor necrosis factor-α, and inhibited antigen recall responses. B cell receptor (BCR) sequencing further revealed that citAg vaccine could dampen the dysregulated V(D)J recombination, restoring the immune repertoire. Taken together, the results demonstrated that citAg vaccine might have a therapeutic effect on RA.