Vanda coerulea, an epiphytic plant with bare roots growing in air, has important value for orchid breeding and ornament. Exploring the development and defense mechanism of the aerial roots from the omics level can provide a theoretical basis for comprehensive understanding of the unique adaptation mechanism of aerial roots. In this study, we used three root sites with different developmental levels of V. coerulea aerial roots as materials, combined with transcriptomics and metabolomics, to reveal the development of different parts of V. coerulea roots and the defense mechanisms. Transcription-metabolism analysis showed that the differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) were significantly enriched in the metabolic pathway, biosynthesis pathway of various secondary metabolites and pathway of plant hormone signaling in two comparison groups. Transcriptome analysis showed 11 995 DEGs between the meristematic (group A) and elongation (group B) zones of the root, with 6274 up-regulated and 5721 down-regulated. There were 3673 DEGs between the elongation (group B) and maturation zone (group C) of the root, with 1691 up-regulated and 1982 down-regulated. Metabolomic results revealed 102 DAMs between the two comparison groups, with 52 up-regulated and 50 down-regulated. In the development of roots, the relative expression levels of growth regulators such as auxin, gibberellins (GAs) and abscisic acid (ABA) had significant changes in different developmental stages of plant roots. In terms of defense mechanism, the genes related to the synthesis of alkaloids, flavonoids, and lignins were more expressed in the meristem and elongation zone of roots than in the mature zone. The results indicate that aerial roots development under the regulation of the above-mentioned hormones and accumulate a variety of secondary metabolites to improve defensive capabilities.