Despite the development of new diagnostic and advanced treatment strategies, the prognosis of patients with osteosarcoma remains poor. It is thus urgent to identify novel and effective targets and treatment regimens for osteosarcoma patients. In this study, we found that super-enhancer-associated genes contribute to the malignant potential of osteosarcoma. Knockdown of CDK7 reduced the phosphorylation of the RNA polymerase II (RNAPII) C-terminal repeat domain (CTD), which is enriched in super-enhancers and suppresses osteosarcoma cells. THZ2, a new specific CDK7 inhibitor, selectively suppressed super-enhancer-associated genes, especially oncogenes, through inhibiting the activity of CDK7 by covalent binding. This newly developed small molecular inhibitor, THZ2, exhibited a powerful anti-osteosarcoma effect in vitro and in vivo. Our findings provide an important molecular foundation for understanding the pathogenesis of osteosarcoma through super-enhancers. They also indicate that targeting super-enhancer-associated oncogenic transcriptional programs with a specific CDK7 inhibitor, THZ2, may be a promising therapeutic strategy for patients with osteosarcoma.