The notable absence of juvenile Pseudolarix amabilis trees in forest understories suggests their vulnerability to ecological niche competition, leading to limited survival prospects. This study examines the key factors limiting the growth of P. amabilis seedlings by investigating the effects of five ecological factors: light intensity, rainfall, groundwater level, soil type, and type of fertilization, on the growth of one-year-old P. amabilis seedlings. Our results demonstrate that increasing the light intensity promotes plant growth by augmenting the leaf count, leaf biomass, plant height, stem biomass, root biomass, and total biomass. Further analysis reveals that increased light intensity influences biomass allocation, reducing the specific leaf area and leaf–stem biomass ratio, and favoring root and stem growth over leaf investment. Rainfall, groundwater level, fertilization type, and rhizosphere soil type primarily influence root growth by impacting the soil’s physicochemical properties. Specifically, rising groundwater levels lower the soil temperature and increase the soil moisture, total potassium content, and soil pH, leading to reductions in root biomass, plant height, net height increment, leaf number, and total biomass. When groundwater levels reach 21 cm and 28 cm, submerging the surface soil layer, root biomass decreases by 1.6 g/plant (−51.6%) and 2.3 g/plant (−74.2%), respectively. Further analysis reveals a gradual decrease in the root–shoot ratio above the 14 cm groundwater level, while the specific leaf area and leaf–stem biomass ratio remains unaffected, indicating stronger belowground root stress compared to aboveground stem and leaf components. The results highlight light intensity as the key ecological factor determining the growth of P. amabilis seedlings. These findings underscore the importance of considering light intensity in the management of natural stands, the cultivation of artificial forests, and the nursery cultivation of endangered P. amabilis.