Abstract: This study evaluated how integrated tree-management practices affect seed yield and seed quality in Chamaecyparis hodginsii (Dunn) Rushforth, with the goal of providing practical guidance for standardized seed orchard management and improved variety cultivation. A single clone of C. hodginsii mother trees established in 2014 at Fengtian State-owned Forest Farm, Anxi, Fujian Province, was used as experimental material. An L9 (3⁴) orthogonal design was applied using three management factors: stumping height, pruning intensity, and girdling intensity, each set at three levels to generate nine treatment combinations. Seed yield, seed quality, and physiological and biochemical traits were measured, and Pearson correlation analysis was used to assess associations between yield and quality-related indices. Results showed that tree-management practices significantly improved both seed yield and seed quality. The A₂B₂C₁ combination produced the highest cone yield, seed yield, soluble protein content, germination index, superoxide dismutase (SOD) activity, catalase (CAT) activity, and malondialdehyde (MDA) content, increasing these indices by 101.42%, 178.76%, 215.56%, 66.47%, 282.77%, 206.50%, and 245.71%, respectively, compared with the control. The A₂B₂C₂ combination produced the highest 1 000-seed weight, with a 102.69% increase relative to the control. Comprehensive evaluation of seed yield and quality identified stumping height as the dominant factor regulating seed development in C. hodginsii. Overall, A₂B₂C₁, consisting of a 2-m stumping height, 20% pruning intensity, and single-ring girdling, was the most effective management regime for improving seed orchard productivity and seed quality.