Tolerogenic dendritic cells (tolDCs) have the potential to treat rheumatoid arthritis (RA) by inducing immune tolerance. However, the mechanism of intervention needs further study. Here, we investigated whether tolDCs formed microchimerism and their effect on the expression of immune checkpoint molecules after infusion of tolDCs into rats with collagen-induced arthritis (CIA). TolDCs derived from male SD rats were labeled with fluorescence and infused into female CIA rats. The fluorescence signals as well as the sex-determining region of Y-chromosome (SRY) gene revealed that tolDCs formed microchimerism in the mesenteric lymph nodes and ankle joints. We further explored the effect of tolDCs on the expression of immune checkpoint molecules in mesenteric lymph nodes and ankle joints. For stimulatory immune checkpoint molecules, the expressions of CD86 and CD40 decreased in mesenteric lymph nodes, and the expressions of CD40, CD40L, CD28, CD80, and CD86 also decreased in rat ankle joints. In contrast, the inhibitory immune checkpoint molecule PDL1 increased in mesenteric lymph nodes, and PD1, PDL1, and CTLA4 increased in ankle joints. In conclusion, our results suggested that intervention of tolDCs in CIA is associated with the formation of microchimerism and the effect on immune checkpoints.