• After aerated drip irrigation, soil oxygen content significantly increased. • The duration and sequence of aeration changed the root antioxidant system. • The root antioxidant system correlated root morphology of tomato. • Root antioxidant systems and growth affect water and nitrogen uptake efficiency of tomato. China has the largest area of vegetable cultivation in greenhouse vegetable system in the world. However, the excessive application of irrigation and fertilizers has caused soil degradation and hardening, even leading to injury and yield loss in vegetable. Increasing soil aeration oxygen can improve crop water and nutrient uptake efficiencies. However, its effects on crop antioxidant systems are less known. Due to the sensitivity of the antioxidant system to changes in soil oxygen content, it is expected that aerated drip irrigation (ADI) delivering microbubble water to the crop rhizosphere will alter root antioxidant enzyme activities, malondialdehyde (MDA) content, and osmotic regulators in tomato plants. We conducted pot experiments under eight irrigation regimes: five aerated durations (0%, 25%, 50%, 75%, and 100%) of the subsurface drip irrigation period aerated (CK, A 25% , A 50% , A 75% , and A), with two aerated sequences (L: subsurface drip irrigation follow by aerated drip irrigation, F: aerated drip irrigation follow by subsurface drip irrigation) for the A 25% , A 50% and A 75% treatments. All treatments with ADI had an average of 7.63% higher oxygen concentration (OC) than the CK treatment at 74 d after transplanting. The principal component analysis revealed that MDA of all treatments had the greatest effect on the antioxidant system, while aerated drip irrigation reduced MDA content. Increasing aeration duration from A 25% to A 75% significantly affected antioxidant enzyme activities and root growth parameters, and the L treatment had higher values than the F treatment. The L -A 75% treatment had the highest water use efficiency, nitrogen uptake efficiency, and yield. The structural equation model demonstrated that ADI indirectly promotes tomato water and nitrogen uptake efficiencies by affecting the antioxidant system and root growth.