Plantations of the valuable Chinese timber species, Chamaecyparis hodginsii, established by planting, primarily rely on seed orchards for propagation. Therefore, effective management of the genetic composition of these orchards is essential to ensure a sustainable supply of high-quality seeds. However, the mating system and pollen dispersal mechanisms in its high-generation seed orchards remain unclear, limiting precise genetic management. To address this, we analyzed 30 parental clones and 75 of their open-pollinated progeny from a second-generation seed orchard using 15 polymorphic EST-SSR markers. Compared to reported natural populations of C. hodginsii, both parental and progeny populations maintained high genetic diversity (mean uHe = 0.438 and 0.449, respectively), with a significant excess of heterozygotes (mean Fis = −0.084 and −0.066, respectively). Population genetic structure analysis indicated weak genetic differentiation among the parental genetic groups (mean Fst = 0.012), which was further reduced in the progeny population (mean Fst = 0.003) due to open pollination, reflecting a trend toward genetic homogenization. The mating system was characterized exclusively by outcrossing (tm = 1.000). However, paternity analysis revealed highly skewed paternal contributions, a low effective number of pollen donors (Nep = 8.13), and contributions of S5, S11, and S17 as dominant pollen parents, with 17.33% external pollen flow. These findings elucidate the mechanisms underlying sustained genetic diversity despite unequal paternal contributions and provide a theoretical basis for optimizing parental configuration and pollen management.