Weak seedlings and poor growth uniformity affect the mechanical transplanting of densely sown rice seedlings. To address these issues, seedlings of the conventional japonica rice “Zhehexiang 2” were grown in a traditional flat tray (control), pot-mat tray (26 × 52 bowls; BT(26)), and pot-mat tray (30 × 58 bowls; BT(30)) to compare the effects of different specifications of pot-mat trays (BTs) on the growth and quality of mechanical transplanting of densely sown rice seedlings with 250 g/tray. The BT-raised seedlings showed improved seedling quality, with increases in the shoot and root dry weights by 7.44% and 20.11%, respectively, compared to the flat tray. Under the dense sowing rate, the plant height uniformity of the BT(26) and BT(30) treatments was significantly increased by 6.95% and 3.43%, and the root entwining force of the seedlings was 14.28% and 10.21% higher, respectively, compared with those of the control. The missing hill rate for BT-raised seedlings after mechanical transplanting was significantly reduced by 53.15%. The loss of roots during mechanical transplanting was reduced. Compared with the control, the root length, root surface area, and root number were increased, and a greater number of large roots were retained, which promoted the early development of seedlings after mechanical transplanting. The proportion of holes with two to five seedlings was higher after mechanical transplanting. The pot-mat tray divided the root growth area of seedlings, promoted the growth of the seedlings, and reduced the root loss and missing hill rate under the high sowing rate. Thus, the quality of mechanical transplanting of densely sown seedlings was improved.