Pterocarpus santalinus is one of the most famous rosewood (Hongmu) species in the world. Its large-scale development is restricted due to limited seed production in China. A grafted clone seed orchard was established recently using suprior tree materials by Experiment Station of Research Institute of Tropical Forestry, Chinese Academy of Forestry in Jianfengling, Hainan Island, and most trees in the orchard have flowered and fruited. The differences in seed quality among superior trees in the introduction garden and the grafted clones need to be studied. Here the morphological traits were measured, and germination tests were conducted for the seeds of P. santalinus collected from six superior trees in the introduction garden and the grafted clones in the seed orchard at the experiment station. The coefficients of variance for the seed morphological traits were much lower than those for seedling growth traits among superior trees or the grafted clones, and the coefficients of variance was the lowest for the weight of 1000-grain seeds, indicating that the variations of seedling growth were more abundant than those of seed morphorlogy Seed length was significantly different at 0.05 level among the superior trees with No. 7 performing the best, and seed length, width and thickness differed remarkably among the grafted clones, in which No. 9^# performed the best in seed length and width, and No. 7^# did the best in seed thickness. The germination rate and potential differed significantly among superior trees (No. 3 and No. 9 performed the best, respectively) or the clones (No. 5^# did the best), and significant difference occurred in the length of epicotyl, hypocotyl, radicle and total seedling among the superior trees (No. 3 did the best), and in the length of radicle and total seedling among the grafted clones (No. 7^# did the best), demonstrating that abundant variation in seed germination and seedling growth existed among superior trees and among the grafted clones. Significance of difference between each superior tree and its clone varied with gene type, and clones performed as a whole, better than relevant superior trees in seed length and width, seed germination and seedling growth. It was indicated from relationship analysis that seed weight was significantly correlated with germination rate at 0.01 level, the germination rate of the plumper seeds was higher. In conclusion, seeds from the grafted clone seed orchard performed better in the seed morphorlogy and germination than those from the superior trees in the introduction garden, and significant difference was absent in seed weight among the superior trees or the grafted clones, and between each superior tree and its clone (P≥0.05), the seeds developed fully in the seed orchard with 1000-grain weight near 100 g, more than that for scattered individuals early grafted (92.9 g). The findings would provide scientific evidences for elite variety selection, seed orchard establishment and robust seedling cultivation.