Seedling raising has been one of the most key steps in the process of rice mechanization production. In this study, a fully automatic palletizer of a rice seedling tray was designed to accurately clamp, transfer, and position the rice seedling trays in the rice factory. A Cartesian coordinate structure was selected to design the key components, according to the basic structure and working principle of the palletizer. A Programmable Logic Controller (PLC) was utilized as the control core, further to construct the hardware circuit and software program of the system. A palletizing layer detection of the rice trays was designed using the PLC. Specifically, the height of palletized trays was detected to determine the number of completed layers in the control system, thereby realizing the accurate palletizing of rice trays. The optimal ranges of the principal factors were then determined for better palletizing performance. A Box-Behnken orthogonal combination test was conducted to clarify the relationship between the main influencing factors of the operational performance (productivity, detection time of the palletizing layer detection mechanism, and the tray releasing height) and the palletizing performance indexes (palletizing passing rate and seed exposure rate). The influencing factors on the palletizing pass rate were ranked in the descending order of the detection time and tray height. Once one variable was fixed, there was a trend of first rising and then smoothing in the influence of the rest two parameters on the palletizing passing rate. Compared with the productivity, the tray height presented an outstanding influence on the seed exposure rate, indicating a trend of first rising and then falling. A multi-objective optimization was used to optimize the parameters, the influence of each factor, and the interaction on palletizing performance indexes. The test results showed that the detection time and the releasing height of the palletized trays presented a greater effect on the palletizing pass rate, whereas, the releasing height of the palletized trays, productivity and detection time presented a greater effect on the seed exposure rate. An optimal combination of parameters was 1.15 s for the testing time, and 1.10 cm for the releasing height. Correspondingly, the productivity was adjusted to 400, 500, and 600 trays/h under the optimal combination of parameters, where the palletizing pass rates were 99.33%, 99.50%, and 99.20%, respectively, and the seed exposure rates were 0.40%, 0.53%, and 0.70% respectively. Once the productivity was 400-600 trays/h, the palletizing pass rate was greater than 99%, and the seed exposure rate was lower than 1%. The rice planting automation can be widely expected to realize in the precision seeding production for rice seedling transplanting.