Soil compaction easily causes root hypoxia stress, resulting in poor root growth and the absorption of soil water and nutrients. We hypothesized that aerated irrigation (AI) could enhance nutrient uptake and utilization, thus unlocking the high yield potential by increasing soil aeration and root morphology indicators compared with that in the non-aeration treatment. A greenhouse experiment was conducted to investigate the effect of soil aeration and root morphology on the yield of greenhouse cucumbers. The dissolved oxygen (DO) in irrigation water at 10 mg L−1 (A1), 20 mg L−1 (A2), and non-aeration treatment (A0) were applied via a subsurface drip irrigation system. The soil respiration rates, DO in soil water, root morphology, and crop yield were measured. The results showed that AI could significantly improve the soil respiration rate, DO in soil water, and root morphology compared with non-aeration treatment. The A2 significantly increased soil respiration rate by 11.63% and 11.93%, respectively, compared with the A1 and A0 treatments. Under A1 and A2, the DO in soil water increased by 20.01% and 18.02%, respectively, compared with the A0. Moreover, during the flowering and fruit set, the mature, and the late stages, the root surface area, root volume, root tip number, root forks, and root dry weight in the A2 treatment significantly increased than that in the A0 treatment. The soil respiration rate, DO in soil water, root length, and root forks were the main indexes correlated to the yield, respectively. The DO in soil water and root forks number significantly influenced the yield. The cucumber yield and economic benefits in A2 peaked at 53.04 t ha−1 and 3.95 × 104 USD ha−1, increased by 7.86% and 7.30% compared with that in the A0 treatment, respectively (p < 0.05). The results could provide technical support and scientific knowledge for regulating greenhouse cucumbers under AI.
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