Cunninghamia lanceolata (Chinese fir) is an important industrial coniferous timber tree in southern China with high yield and excellent wood traits. Brassinosteroids (BRs), a class of polyhydroxylated steroidal hormones, play critical roles in the formation of wood, which is the most abundant biomass produced by plants. However, the molecular regulatory network of BR-mediated wood formation remains largely uncharacterized in coniferous trees, especially in Chinese fir. To this end, systematic identification and characterization of the BES1/BZR1 transcription factor (TF), the specific BR-responsive TF, were performed. Seven ClBES1/BZR1 members were screened and distributed on four chromosomes. ClBES1/BZR1s showed various expression profiles in different tissues and growth stages. ClBES1/BZR1–1, a hub gene in BR-mediated xylem development, repressed the transcription activity of ClCCoAOMT and ClMYB3 by directly binding to their promotors. Furthermore, ClBES1/BZR1–1 overexpression significantly decreased the lignin biosynthesis and xylem differentiation compared to wild-type. In contrast, ClBES1/BZR1–1 dominant repression greatly promoted lignin deposition during secondary cell wall (SCW) development. Consequently, by repressing the lignin-related genes’ expression, ClBES1/BZR1–1 negatively regulated the SCW deposition and xylem development in Chinese fir. These findings shed light on the regulatory role of BR modulating lignin accumulation during wood formation.