Human Dihydroorotate dehydrogenase (HsDHODH) is a flavin-dependent mitochondrial enzyme, which has been certified as a potential therapeutic target for the treatment of rheumatoid arthritis and other autoimmune diseases. Based on lead compound 4, which was previously identified as potential HsDHODH inhibitor, a novel series of thiazole derivatives were designed and synthesized. The X-ray complex structures of the promising analogues 12 and 33 confirmed that these inhibitors bind at the putative ubiquinone binding tunnel and guided us to explore more potent inhibitors, such as compounds 44, 46 and 47 which showed double digit nanomolar activities of 26 nM, 18 nM and 29 nM, respectively. Moreover, 44 presented considerable anti-inflammation effect in vivo and significantly alleviated foot swelling in a dose-dependent manner, which disclosed that thiazole-scaffold analogues can be possibly developed into the drug candidates for the treatment of rheumatoid arthritis by suppressing the bioactivity of HsDHODH.