Rapeseed (Brassica napus) is one of the most important oil crops worldwide and provides a major source of edible vegetable oil. Currently, manipulating plant height with branching effectively balances biomass and yields. However, the genetic mechanisms to control plant height remain largely unknown in rapeseed. To address this gap, we isolated an extremely dwarf mutant (dm1) from ethyl-methanesulfonate (EMS) mutagenesis and revealed that the dwarfism results from a significant reduction in cell length. Bulk segregant analysis (BSA) identified BnaA10.CYP90A1 and BnaC09.CYP90A1 as the causative genes of dm1. Both genes encoded the proteins homologous to the Arabidopsis cytochrome P450 AtCPD/AtCYP90A1, which is crucial for brassinosteroid (BR) biosynthesis. In this regard, we demonstrated reduced levels of bioactive BRs, castasterone (CS), and its precursor 6-deoxoCS in dm1, resulting in down-regulation of various genes involved in cell expansion. The reduced BR levels also caused negative feedback, promoting the expression of BR biosynthetic genes in dm1. Furthermore, we proved that the single mutation of BnaA10.CYP90A1 gene conferred semi-dwarfism, potentially beneficial for producing an ideal type of plant to improve cultivars with a balance of yield and machinery harvest through genetic modifications. Collectively, these findings highlighted the critical role of BnaCYP90A1s in BR biosynthesis and validated their influence on plant height regulation in rapeseed.