To increase the cannabidiol (CBD) content of industrial hemp, male hemp was screened out by spraying cytokinin at the three-leaf stage of seedlings, and more female hemp was cultivated. 6-BA 60 mg·L treated female flowers of industrial hemp were subjected to transcriptomic, proteomic, and metabolomic analyses to investigate the changes and molecular mechanisms of gene expression and metabolites and related pathways of 6-BA in the development of female flowers of industrial hemp. The results showed that 1189 differentially expressed genes (DEGs), 168 differentially expressed proteins (DEPs), and 138 DAMs were screened compared with the control. Functional enrichment analysis revealed that phytohormone signaling, starch and sucrose metabolism, flavonoid biosynthesis, phenylpropane metabolism, and glutathione metabolism were the major pathways enriched, and differential genes, proteins, and metabolites enriched in the above pathways were further followed up and analyzed. It was found that, among them, , and C4H were the key genes and proteins involved in the phenylpropane metabolic pathway, and were not only the upstream genes in the flavonoid biosynthesis pathway, but were also involved in the synthesis of phytohormones and catabolism. was related to the synthesis of saccharides. It was hypothesized that the carbohydrates might synergistically act with cytokinins to induce female flower differentiation in industrial hemp. The flavonoid biosynthesis pathway and glutathione metabolism pathway are also closely related to feminization. This paper provides a reference for subsequent studies on sex differentiation in hemp or other plants.