Abstract: High-quality seedlings can greatly contribute to optimal plant growth, crop yield, and the overall efficiency of plant production. The ever-increasing demand has often required for high-quality seedlings in recent years, with the rapid development of the plant factories. Among them, the roots are the most significant organ of the seedlings to uptake nutrients and water. More extensive root biomass accumulation has been widely characterized by strong seedlings. Taking the accumulation of root biomass as the main objective, this evaluation criteria can be expected to be selected for the strong seedlings. This research aims to clarify the effects of the irrigation mode on strong seedling cultivation and growth after transplanting of hydroponic lettuce in LED plant factories. Two irrigation modes (deep liquid (DL) and aeroponic (AE)) were set for seedlings. DL mode was used to maintain a nutrient solution depth of 90 mm to support root growth. AE mode set the height of root growth space at 198 mm and sprayed nutrient solution for 15 s every 10 min. The most commonly used low liquid was taken as the control group (CK), with only a 20mm depth of nutrient solution for root growth. A comparison was made to explore the effects of the irrigation mode on the lettuce growth during seedling after transplanting. The results showed that the depth of the nutrient solution around lettuce roots significantly enhanced the seedling root biomass accumulation and shoot fresh weight. Specifically, the DL shared the highest diameter of the seedling stem, leaf area, true leaf number, shoot fresh weight, root fresh weight, shoot dry weight, total root length, root surface area, root volume, forks, and seedling index. Furthermore, the DL mode significantly improved the leaf area by 41.7% and 23.7%, and the root fresh weight by 50.0% and 36.4%, respectively (P<0.05), compared with the CK and AE. Shoot fresh weight of the DL mode was significantly promoted by 40.0% (P<0.05). The DL mode significantly improved the total root length by 34.9% and 60.4%, and the root surface area by 42.6% and 45.7%, respectively. Additionally, the DL shared the highest root morphology, except for the root average diameter and root tips. The root average diameter of the AE was significantly improved by 16.7% (P<0.05), compared with the CK. There was no significant difference from the DL. In the seedling index, the DL shared the highest value with increases of 143.3% and 51.5%, compared with the CK and AE, respectively. The root activity of AE was significantly increased by 54.4%, compared with the DL. The largest canopy of the DL was found with a growth advantage 28 days after transplanting. The shoot fresh weight significantly increased by 55.1% and 42.9%, respectively, compared with the CK and AE (P<0.05). Furthermore, the root surface area, root volume, and root tips also significantly increased by 24.4%, 40.7%, and 58.0%, compared with the CK (P<0.05). The correlation analysis showed that the shoot fresh weight 28 days after transplanting was highly positively correlated with the seedling root morphology, except for the root average diameter. Specifically, the total root length, root surface area, root volume, and forks were extremely significantly correlated with the shoot fresh weight (P<0.01), while the root tips were significantly positively correlated with the shoot fresh weight (P<0.05). In summary, the deep liquid significantly promoted strong seedling cultivation for the shoot fresh weight. A suitable irrigation mode can be expected to serve as the lettuce production for the economic benefits in the production of plant factories. Furthermore, the aeroponic also showed potential for strong seedling cultivation. It is necessary to develop special devices for seedling cultivation in sustainable agriculture.