Aristolochic acids (AAs) and their derivatives are present in multiple Aristolochiaceae species that have been or are being used as medicinal materials. During the past decades, AAs have received increasing attention because of their nephrotoxicity and carcinogenicity. Elimination of AAs from medicinal materials using biotechnological approaches is important for improving medication safety. However, it has not been achieved because of the limited information available on AA biosynthesis. Here, we report a high-quality, reference-grade genome assembly of the AA-containing vine Aristolochia contorta. The total size of the assembly is 209.27 Mb, and it is assembled into 7 pseudochromosomes. Synteny analysis, Ks distribution, and 4DTv suggest an absence of whole-genome duplication (WGD) events in Aristolochia contorta after the angiosperm-wide WGD. Based on genomic, transcriptomic, and metabolic data, pathways and candidate genes were proposed for benzylisoquinoline alkaloid (BIA) and AA biosynthesis in A. contorta. Five O-methyltransferase genes, including AcOMT1-3, AcOMT5, and AcOMT7, were cloned and functionally characterized. The results provide a high-quality reference genome for AA-containing species of Aristolochiaceae. They lay a solid foundation for further elucidation of AA biosynthesis and regulation and for the molecular breeding of Aristolochiaceae medicinal materials.