Tea (Camellia sinensis) leaves are used to make the most widely consumed beverage globally after water. Therefore, the safety and quality of raw tea leaves are important indices for making tea and related products. Habitat management has been widely used as an environmentally friendly method to control pests in agroecosystems. To investigate the impact of habitat management on tea plantation ecosystems, a habitat management approach with intercropping was established. The function of habitat management on pest control was evaluated. Furthermore, metabolome and transcriptome analysis were applied to assay changes in quality-related metabolites. The habitat management approach was found to maintain arthropod biodiversity and develop natural arthropod enemies in the tea plantation. Therefore, the yield of the habitat management-treated tea plantation was increased. Metabolome analysis showed that epigallocatechin-3-gallate, the major catechin in tea leaves, has a significantly increased content in leaves of tea plants under habitat management compared with those in the control tea plantation. The content of L-theanine, the major amino acid in tea leaves, was not significantly changed in tea plants under habitat management. Furthermore, aroma compounds were more abundant in tea leaves from the habitat management-treated tea plantation than those from the chemical pesticide-treated tea plantation. Therefore, habitat management is reported for the first time as a safe and effective approach to improving the yield and quality of tea leaves.