Cinnamomum burmannii is an important medicinal and industrial plant as its key source for natural borneol (D-borneol), one of the precious materials and widely used in the pharmaceutical and cosmetic industries. Here, we report a high-quality chromosome-scale genome assembly of Mei Pian Tree (C. burmannii (chvar. Borneol)), a chemotype of C. burmannii containing high content of natural borneol. The assembled genome size was 1.14 GB with a scaffold N50 of 94.30 Mb, while 98.77% of the assembled sequences were anchored on 12 pseudochromosomes including 41549 protein-coding genes. Comparative genomic analysis revealed C. burmannii and C. micranthum，shared two Lauraceae unique ancestral whole-genome duplication (WGD) events, and strong collinearity was detected between these two species. The analysis for repetitive sequence indicated the outbreak of LTR-RTs insertion made a great contribution to the size difference of genomes between C. burmannii and C. micranthum. Pathways and transcriptome analysis demonstrated differential expression of genes involve in MEP may be the main factors for D-Borneol production differences between the two chemotypes (chvar. Borneol/Wild). We also identified and their differential expressions were further analyzed in various biological tissues. Finally, we constructed the genome database (CAMD; http://www.cinnamomumdatabase.com/) of Cinnamomum species. The present study provided the first high quality genome of C. burmannii and comprehensive analysis of the biosynthesis pathway of natural borneol. We also provided novel insights into the molecular basic for chemotypes. These results will shed light on the understanding of the evolution of Lauraceae plants and genetic improvement of this commercially important plant.