With global warming, the frequency and duration of drought is becoming longer and longer, which seriously affects the survival of trees. Light intensity control, such as shading, is an important measure in seedling nurseries. However, it is unclear whether early shading affects the drought tolerance of seedlings used in afforestation. We conducted a two-stage experiment on Pinus yunnanensis seedlings. First, three different shading treatments were set, namely HL (0% shading), ML (55% shading), and LL (80% shading). After 90 days of cultivation, the seedlings of each shading treatment were subjected to CK (water content of 90% ± 5%), LD (water content of 75% ± 5%), MD (water content of 60% ± 5%) and SD (water content of 45% ± 5%) continuous drought for 30 days. The contents of non-structural carbohydrates (NSCs), carbon (C), nitrogen (N), and phosphorus (P) and their ratios in the needles of P. yunnanensis seedlings were measured. Early shading affected the starch accumulation and the balance between C absorption and consumption in P. yunnanensis seedlings during drought. Early shading affected C consumption, P utilization efficiency, and N restriction under drought stress. The phenotypic plasticity index showed that the plasticity of P. yunnanensis seedlings under drought stress followed the order: LL >
HL >
ML. The results of principal component analysis showed that the performance under drought stress followed the order HL >
LL >
ML. These results indicated that early shading could affect the response of P. yunnanensis seedlings to drought. The P. yunnanensis seedlings grown under HL and LL were more resistant to drought stress than those grown under ML. It is suggested that 0% or 80% shading should be applied at seedling stage to improve the drought resistance of P. yunnanensis.