In order to promote the ebb and flow irrigation technology in vegetable seedling production and select an optimal ebb and flow irrigation system for tomato, an L₄(2³) orthogonal experimental design was conducted using ‘Yingfen No. 8’ tomato. Tomato plug seedling growth, physiological changes, matrix properties, and irrigation indexes were analyzed. The results showed that tomato seedling growth, seedling index, photosynthetic efficiency, and root activity of T3 were the highest. Compared with the top sprinkling irrigation (T1 and T2), the EC of the substrate and the irrigation volume of the ebb and flow irrigation treatments (T3 and T4) were the lowest. Irrigation frequency was the most important factor affecting plant fresh weight, plant dry weight, G value, net photosynthetic rate, and root activity, while irrigation method was the most important factor affecting the irrigation amount. In summary, the optimal irrigation system for tomato seedling production was A2B1C2, i.e. using the ebb and flow irrigation method at the irrigation frequency of 1 time/2 d and irrigating plants in the afternoon (16:00).