Taking 76 individuals selected from the F1 progeny seedlings of 22 artificial hybrid combinations of Taxodium Rich. as materials, the variation, genetic diversity, correlations, parental combination effects, and phenotypic group differentiation of 24 phenotypic traits were systematically evaluated. The results show that the coefficients of variation for leaf arrangement, leaf shape, lateral branch orientation, and lateral branch arrangement in Taxodium hybrid progenies are relatively large (greater than 106%), indicating strong plasticity; the Shannon-Wiener indexes of tree height, crown shape, and leaf color in autumn (mid-November) are relatively high (which are 1.94, 1.58, and 1.54, respectively), indicating evident differentiation. The correlation analysis result shows that lateral branch width, leaf angle, and leaf length exhibit extremely strong positive correlations, but they all show strong negative correlations with tree height, reflecting resource allocation trade-offs; leaf color in autumn (mid-November) and winter (mid-December) show moderate negative correlations with defoliation stage, revealing their physiological associations. The parental combination effect analysis result shows that the progenies of T. mucronatum Ten. × T. distichum var. imbricatum (Nutt.) Croom exhibit superior performance in tree height, diameter at breast height, defoliation stage, leaf shape, leaf density, leaf arrangement, and red blight resistance, while the progenies of the backcross combination T. ‘Zhongshanshan’ × T. mucronatum generally show inferior performance, and T. distichum (Linn.) Rich. parents play a dominant role in leaf color in autumn and winter. The cluster analysis divides the 76 progeny individuals into four groups, among which group 2 (excellent comprehensive trait type) is identified as the core group for multi-objective breeding; group 4 (balanced ornamental type) exhibits excellent crown shape and leaf color in autumn and winter, suitable for landscape selection; group 3 (tall and late-defoliation type) has a larger scale and outstanding diameter at breast height growth, which could serve as a supplementary source of fast-growing materials. In conclusion, in Taxodium hybrid breeding, parents with greater genetic distance should be preferentially selected for hybridization to maximize heterosis. In the early selection stage of superior groups, on the basis of prioritizing group 2, individuals with excellent comprehensive performance from group 3 could be further selected as supplementary materials.