<p>As a rare and endangered species, <i>Primula filchnerae</i> Knuth faces high seedling-stage mortality that likely contributes significantly to its threatened status. The study aims to investigate the effects of different light intensities under controlled conditions on the photosynthetic traits of <i>P. filchnerae</i> seedlings, elucidate its mechanism of light response and identify optimal light environments for seedlings survival, thereby providing a basis for scientific protection. The three light-intensity treatments were established through artificial shading to simulate the constant light intensity of natural habitat conditions observed in the field: intermediate light intensity (L1, 162 µmol·m⁻²·s⁻¹, control), semi-open area (L2, 324 µmol·m⁻²·s⁻¹) and understory (L3, 5.4 µmol·m⁻²·s⁻¹). Our study revealed that <i>P. filchnerae</i> seedlings exhibited significantly reduced Pnmax and PI_ABS under both L2 and L3 treatments relative to L1. Specifically, the decrease in photosynthetic rate under L2 was caused by stomatal limitation, while that under L3 was induced by non-stomatal limitation. In contrast, <i>P. filchnerae</i> seedlings maintained high antioxidant enzyme activity and stable accumulation of osmoregulatory substances in L1 treatment. Transcriptomic profiling indicated that flavonoid biosynthesis pathway genes were highly expressed under L2 compared to L1, while photosynthesis-related genes were downregulated under L3 condition. Based on the findings, the L1 treatment represents the optimal growth condition for <i>P. filchnerae</i> seedlings, where photosynthetic efficiency, light energy utilization capacity and stress resistance achieve their most favorable synergistic state. In contrast, both the L2 and L3 conditions were shown to be suboptimal, adversely affecting seedlings growth and physiological performance.</p>