The paper aims to research the effects of different cell volumes of trays on tomato, cucumber and broccoli. We investigated the effects of four types of trays (32- cell, 50- cell, 72- cell and 105- cell with volumes of 110, 55, 40 and 32 cm3, respectively) on the seedling index, leaf photosynthesis and root growth in tomato, cucumber and broccoli seedlings. The results showed that the seedling index was decreased in 105- cell trays for all the three kinds of vegetables. Compared with seedlings grown in 32-cell trays, the seedling index in 105-cell trays was decreased by 67.45%, 42.20% and 68.22% in tomato, cucumber and broccoli, respectively. However, the seedling index of tomato plants grown in 32-cell, 50-cell and 72-cell trays had no significant difference and so did the seedling index of cucumber plants. The seedling index of broccoli was significantly higher in 32-cell trays compared with that in 50-cell and 72-cell trays (P<0.05). In comparison with plants in 32- cell trays, the actual photosynthetic efficiency (ΦPSII) of vegetable seedlings decreased significantly in 105- cell trays (P<0.05), which was due to the reduce of qP. Interestingly, there were no significant differences in ΦPSII among vegetable plants grown in 32-cell, 50-cell and 72-cell trays. Compared with plants grown in 32-cell trays, the root dry mass of tomato, cucumber and broccoli grown in 105-cell trays was decreased by 65.21%, 57.69% and 76.03%, respectively. Meanwhile, the total root volume was decreased by 51.24%, 27.86% and 70.30%, respectively, and the number of apical was decreased by 67.40%, 29.23% and 67.87%, respectively. These results indicate that the 105-cell tray limits the root growth, reduces the leaf photosynthetic electron transport rate, and thus decreases the crop biomass and seedling index. Fortunately, the above results are not found in 50-cell and 72-cell trays, which are suitable for industrialized cultivation.