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To ensure sustainable forestry, it is important to establish efficient management procedures for seed orchards. We evaluated the effects of thinning, pruning season and girdling intensity on tree growth and vigor in an old <i>Larix</i> <i>kaempferi</i> seed orchard. Even after four years, tree size (crown width and tree height) increased, resulting in light intensity of an un-thinned class decreasing. Thinning counteracted the decrease in light intensity associated with tree growth, but it had no effect on promoting tree growth. Tree crown status was scored based on vigor and health. No significant difference in crown vigor was observed between unpruned and winter-pruned trees, but the summer-pruning class showed significantly lower vigor. Five years after girdling, trees with low and moderate girdling levels maintained high crown vigor, similar to intact trees, while the crown vigor of trees subjected to severe girdling was significantly lower. This is the first study to quantitatively model trends in remaining girdling depth over time, and to show that the half decay period was ca. 2–3 years. Our findings suggested that management procedures that combine moderate-level girdling, winter pruning and thinning to maintain rPPFD at 50% are well-suited to balancing tree vigor and reproduction in seed orchards.