Boron (B) is an essential element for plant growth and development as it regulates numerous biological processes. Despite years of research on the role of B in regulating plant growth, changes in cell wall composition due to B deficiencyremain unclear. Here, we study B deficiency on the physiology and transcriptome of Neolamarckia cadamba, a fast-growing woody plant with diverse applications. B deficiency induces severe morphological and anatomical changes in N. cadamba including reduced seedling growth, significant inhibition of shoot tip growth and leaves. B deficiency also resulted in oxidative damage and decreasing B concentration in plant. In addition, enhancing activation of the phenylalanine ammonia lyase (PAL) and phenylpropanoid biosynthesis pathways resulted in increased shoot tip lignification. Pectin content decreased and the genes related to the synthesis of pectin and cellulose in mature leaves of N. cadamba changed expression levels in response to B deficiency. Moreover, BOR1, a potential B transporter, was differentially over-expressed under B deficiency in different tissues. Taking together, we can conclude that adaptive changes in N. cadamba cell walls to respond to B deficiency can potentially be utilized for genetic engineering and breeding for low B tolerance.