Root morphology and growth conditions are crucial for improving plant growth, yield, nutrient efficiency, antioxidant activity, and post-harvest longevity. Root-air-pruning (RAP) in soil-based cultivation promotes the development of lateral roots and root hairs, resulting in denser and healthier root systems. To apply the RAP technique in hydroponics, we utilized a newly designed hydrophobic sponge to introduce air into the root zone. This method stimulates the development of lateral roots, leading to increased nutrient absorption and improved plant health. Our findings show significant increases in shoot biomass, with a 238 % increase in fresh shoot weight compared to control conditions. Chlorophyll content and antioxidant levels were also markedly higher in RAP-treated plants, with antioxidant activity reaching 95% DPPH inhibition compared to 60% in control plants. Additionally, RAP effectively reduced algae growth in nutrient film technique (NFT) systems, lowering maintenance costs and minimizing environmental impact. Metabolomic analysis revealed an enriched phytochemical profile in RAP-treated Pak choi plants, with elevated levels of health-promoting compounds such as flavonoids and phenolic acids. Our study demonstrates RAP as a promising technique for hydroponic farming, offering a sustainable approach to boost yields, enhance nutritional value, and improve efficiency. By addressing key challenges in hydroponic cultivation, RAP technique contributes significantly to more environmentally friendly and economically viable agricultural practices.