This study aimed to investigate the efficacy of micro-nano ozone water technology in alleviating continuous cropping obstacles in facility-grown lettuce. A peat substrate that was previously used for two consecutive lettuce cropping cycles was employed again in a third cultivation cycle. Four treatments were applied in the experiment: continuous cropping substrate irrigated with clear water (T1), continuous cropping substrate irrigated with ordinary ozone water (T2, ozone concentration of 2 mg/L), continuous cropping substrate irrigated with micro-nano ozone water (T3, ozone concentration of 2 mg/L), and fresh substrate irrigated with clear water as the control group (CK). A comparison was made on lettuce growth, physiological parameters, root morphology, antioxidant capacity, and substrate health over these treatments. The results demonstrated that continuous irrigation with clear water (T1) significantly inhibited lettuce growth and physiological development. Compared with the CK group, the plant height, spreading width, and stem diameter of lettuce in the T1 group decreased by 6.47%, 6.19%, and 7.30% (P<0.05), respectively, while the fresh weight declined by 5.47%. Continuous cropping severely impaired root architecture, thereby reducing total root length, root surface area, root volume, average root diameter, root tip number, and root fork number by 58.50%, 56.99%, 56.11%, 16.98%, 49.85%, and 18.58% (P<0.05), respectively. Furthermore, root fresh weight and dry weight decreased by 31.08% and 51.79%, respectively. At the physiological level, the T1 treatment disrupted the stability of the photosynthetic apparatus. The photosynthetic electron transport rate declined, deteriorating lettuce quality indicators. Continuous cropping also deteriorated leaf nutritional quality and antioxidant defense systems. Soluble sugar contents dropped by 32.55%, while nitrate content increased by 23.62%. Activities of key antioxidant enzymes, including superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX), and total antioxidant capacity (T-AOC), plummeted by 75.03%, 68.59%, 39.76%, and 66.47% (P<0.05), respectively. This was accompanied by a 51.73% increase in malondialdehyde (MDA), whereas a 114.22% increase was observed in proline (Pro). Both ozone water treatments reduced these adverse effects, particularly performed best in the micro-nano ozone water treatment (T3). In root architecture, the total root length, surface area, volume, tip number, and fork count increased by 133.18%, 108.73%, 95.65%, 55.67%, and 19.35% (P<0.05), respectively, compared with the T1; Furthermore, T3 treatment reduced fungal abundance in the substrate by 91.02%, whereas the urease activity increased by 22.31%, and ultimately lettuce fresh weight and soluble sugar content were improved by 6.73% and 41.14%, respectively, compared with the T1. As such, the ozone water effectively alleviated continuous cropping obstacles for a better rhizosphere microenvironment. Microbial community structure was optimized to promote nutrient transformation. Particularly, micro-nano ozone water (T3) was effective in optimizing root system development, the photosynthetic electron transport chain, and the plant’s antioxidant capacity. The findings can provide a promising theoretical and practical strategy for sustainable practices in facility agriculture.