Abstract Lindera aggregata is a renowned medicinal plant in China, particularly the variety from Tiantai, Zhejiang Province, which is esteemed for its superior medicinal properties. Beyond its medicinal value, it holds significant economic potential and phylogenetic significance. Utilizing a range of sequencing techniques, we have successfully assembled and annotated a high-quality chromosome-level genome of L. aggregata. The assembled genome spans approximately 1.59 Gb, with a scaffold N50 length of 132.62 Mb. Approximately 93.07% of the assembled sequences have been anchored to 12 pseudo-chromosomes, and 70.02% of the genome consists of repetitive sequences. According to the annotations, a total of 33,283 genes are identified, of which 96.95% can predict function. This high-quality chromosome-level assembly and annotation will greatly assist in the development and utilization of L. aggregata’s valuable resources, and also provide a crucial molecular foundation for investigating the evolutionary relationships within the Lauraceae family and the mechanisms behind the synthesis of active ingredients in L. aggregata.