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The seeds cannot fully sprout owing to the seed quality and environmental differences. So it is difficult to provide seedling pots without empty seedling holes for automatic transplanting. In order to reduce the number of seedling shortage and the manual labor intensity of seedling supplement, and to improve transplanting quality, a method for supplementing seedlings in cotyledon phase was presented in the paper. According to the delicate seedling, undeveloped root system and the unconsolidated substrate in pot, a new type of end-effector for supplementing pot-seedling in cotyledon phase with 4 seedling shovels was designed. The 4 angular seedling shovels were synchronously driven up and down by stepper motor moving the X-shaped press rod. They can shape enveloping surface when they are inserted into the lower limit position of the whole pot and surrounded the seedlings from the 4 sides of seedling substrates during seedling. And then the pot seedling was taken out from seedling hole and transplanted to the target hole. The seedling supplementing was finished while the pot seedling was left in the target pot hole and the seedling spades lifted it up along the inclined guide. The 3 factor and 3 level orthogonal tests were conducted respectively with the Zheza809 tomato pot seedlings in cotyledon phase with the seedling age of 16, 21 and 26 d cultivated in standard seedling tray with 72 holes. In the test, the velocities of inserting and taking out of matrix for the shovels were measured by speedtro-50 laser velometer, and the average velocities were 29.85 and 31.12 m/s respectively. The mixture ratio of peat, vermiculite and perlite in nursery matrix, the moisture content of the substrate and the seedling age were chosen as factors. The matrix net rate, which is the percentage of the weight of pot seedling taken out from the pot holes by the end-effector in the total mass of the pot seedling in the pot hole, was set as index. The results indicate that the net rate of taking out the free substrate without seedlings or the pot seedlings in cotyledon phase is affected significantly by the pot seedling age and the mixture ratio of peat, vermiculite and perlite in nursery matrix. The net rate increases with the seedling age, which reaches the highest value at the end of cotyledon phase and the mixture ratio of peat, vermiculite and perlite in nursery matrix of 2:2:1. The effect of matrix water content from 67.1% to 79.2% on the net rate is not significant, while the net rate keeps a high value owing to good cohesive force and plasticity of the substrate when the moisture content of the substrate is 74.1%. When the growth age is 26 d, the mixture ratio of peat, vermiculite and perlite in nursery matrix is 2:2:1 and the moisture content of the substrate is 74.1%, the average net rate reaches the maximum of 89.5% and the shape and volume of the seedling pot keep complete. To further verify the optimal combination obtained by the test, the experiments of seedling taking out and supplementing were carried out with tomato pot seedlings with the age of 26 d, the mixture ratio of peat, vermiculite and perlite in nursery matrix of 2:2:1 and suitable substrate moisture content. The results show that the success rates for the free substrate without seedlings and pot seedlings are both 100%, which can take out the pot seedlings in cotyledon phase with crisp plant and loose matrix as a whole and fill them into target hole on the seedling pot completely. [ABSTRACT FROM AUTHOR]