Abstract: During the mechanical clamping process of automatic grafting machine, grafted seedlings can suffer mechanical damage due to individual variations. To explore the effect of clamping damage on the healing and growth of grafted seedlings, experiments in two stages were conducted using tomato grafted seedlings. First, a compression simulation clamping test was carried out to obtain the mechanical properties and microstructure of seedling stems. Subsequently, using a compression gradient damage method, a post-grafting growth experiment was conducted to analyze the effects of clamping damage on the following: healing survival rate, grafting survival rate, callus tissue morphology, grafted junction morphology, and growth characteristic parameters of grafted seedlings. The results show that at the elastic limit of the scion stem, the average compression force was 4.7 N, and the clamping deformation rate (compression depth divided by the original stem diameter) was 19.87%. At the yield point, the average compression force was 5.29 N, with a deformation rate of 25.73%. Upon entering the plastic stage (deformation rate greater than 25.73%), the medullary cavity tissue collapsed, resulting in cavity formation. When subjected to gradient clamping damage, grafted seedlings exhibited a three-stage growth response. During the elastic stage (deformation rate less than 25.73% and clamping force less than 5.29 N), the grafting survival rate was greater than 90%. Compared to the undamaged group, there were no significant differences in growth characteristic parameters including seedling stem length, rootstock diameter, scion diameter, and vertical plant height (P>0.05). Furthermore, the callus tissue and grafted junction developed normally. In the plastic stage (deformation rate between 25.73% and 60%), cavity damage occurred inside the callus tissue, resulting in a significant decrease in the grafting survival rate. At a deformation rate of 40%, the porosity (the ratio of cavity area to total stem cross-sectional area) was 4.47%, and the grafting survival rate was 70%. During the structural instability stage (deformation rate greater than 60%), both macroscopic epidermal rupture and microscopic cavity damage occurred in the callus, and the grafting survival rate further decreased. When the deformation rate was 80%, the grafting survival rate dropped to 56.67%. However, the healing survival rate remained above 90% across all stages. In summary, clamping damage exhibited a latent characteristic, with internal damage preceding the appearance of any phenotypic symptoms. Although this damage did not affect the healing process of grafted seedlings, it hindered their subsequent growth and development. Based on these findings, it is proposed that the 25.73% elastic deformation threshold serves as a guideline for the reliable operation of the clamping mechanism. Operating within this threshold ensures an acceptable healing and grafting survival rate. Moreover, a conservative safety assessment was conducted to evaluate the elastic threshold, with the clamping gripper designed based on the minimum sampled seedling diameter. Using the maximum scion diameter (3.74 mm) from the statistical normal distribution (range from 2.80 to 3.74 mm) as the worst-case scenario, the assessment confirms that the clamping-induced deformation for all scions remains within the elastic safety zone. The calculated safety limit of 2.78 mm is lower than the actual minimum sample diameter (2.80 mm), which provides an inherent safety margin. These results further demonstrate the robustness of the elastic clamping threshold against natural size variations in factory-grown seedlings. This study provides a theoretical basis for the design and optimization of clamping mechanisms in grafting equipment.