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To achieve high-density tomato seedlings in a plant factory with artificial lighting, tomatoes (<i>Solanum lycopersicum</i> Mill. cv. “Zhongza NO.9”) were used as the experimental material. This study expected to analyze the effects of light intensity (150, 200, 250, and 300 μmol·m⁻²·s⁻¹) and light time (12 and 14 h), as well as daily light integral (<i>DLI</i>, 10.80, 12.60, and 12.96 mol·m⁻²·d⁻¹) and sowing density (50, 72, and 105 holes per tray), on seedling quality. The results indicated that biomass accumulation, seedling quality, and energy use efficiency of seedlings significantly improved with an increase in <i>DLI</i>. At a <i>DLI</i> of 12.96 mol·m⁻²·d⁻¹, seedlings sown at a density of 72 holes per tray exhibited comparable growth characteristics and biomass accumulation to those sown at 50 holes per tray. However, under lower <i>DLI</i>s, seedlings at 50 holes per tray displayed superior growth morphology and seedling quality compared to those at 72 holes per tray. This indicates that increasing the <i>DLI</i> can partially mitigate the negative effects of higher sowing density on seedling quality. Light use efficiency (<i>LUE</i>) and energy use efficiency (<i>EUE</i>) were not significantly different between seedlings at 72 and 105 holes per tray but were higher than those at 50 holes per tray. Therefore, optimizing parameters such as <i>DLI</i> and sowing density can effectively enhance the seedling quality, spatial use efficiency, and light use efficiency in industrial seedling production. Based on the results of this study, a <i>DLI</i> of 12.96 mol·m⁻²·d⁻¹ (achieved with a light intensity of 300 μmol·m⁻²·s⁻¹ and a light time of 12 h) and sowing density of 72 holes per tray are recommended for cultivating high-quality tomato seedlings while reducing energy consumption.