The phenotypic characteristics of forest seeds are the basis of germplasm innovation, genetic improvement, and biological research, and they also are the reference for the development of seed orchards. In this study, we analyzed seed quantity characteristics, phenotypic differentiation, and variation patterns in three seed-bearing clones from different crown layers of the Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) orchard located in Fujian Province, China. We divided the clones into six layers according to crown height and the sunny and shady sides, 14 phenotypic characteristics, and five quality indexes, and we measured the germination rate of seeds. The rate of seeds filled with tannin-like substance in the upper sunny layer was low, but it was high in the lower shady layer. The germination rate was highest in the upper sunny layer and lower in the middle and lower shady sides. Values of most of the 14 phenotypic traits tested differed significantly among clones and layers. The average value of the phenotypic differentiation coefficient was 81.16%, indicating that variation among clones explained most of the total phenotypic variation. The repeatability of the 14 phenotypic traits was high (R > 0.80), indicating that these traits are highly heritable. The phenotypic characteristics of cones and seeds varied from 6.86% to 129.51%. The 14 phenotypic traits exhibited different degrees of correlation, and seed weight, seed circumference, seed width, and seed area can be used to predict other seed traits. However, the correlations between cone traits were not strong. Our results show that when establishing a dwarfing Chinese fir seed orchard, the distribution and variation of seeds in different crown layers of clones should be considered, and clones with more cones in the lower crown layer should be selected as parents.