To investigate the effects of different shade treatments on the growth and non-structural carbohydrates of Pinus yunnanensis seedlings, and to provide a theoretical basis for the cultivation of P. yunnanensis seedlings. In this experiment, the growth, biomass and non-structural carbohydrates (NSC) of P. yunnanensis seedlings were measured by simulating the depressed understory environment and adopting the pot shade method with four shade treatments, 20% shade level (L1), 50% shade level (L2), 70% shade level (L3), 95% shade level (L4), and full light as the control treatment (CK). (1) Shade significantly affected the seedling height, ground diameter, biomass, needle NSC content and thick root NSC content of P. yunnanensis seedlings. With the increase of shade intensity, the seedling height and ground diameter showed a trend of increasing and then decreasing, the biomass showed a trend of decreasing and then increasing and then decreasing, the proportion of needle biomass decreased while the proportion of thick root biomass increased, and the NSC content of needles and thick roots showed a trend of decreasing and then increasing and then decreasing, and the respective shade treatments were all significantly lower than the CK treatment, the percentage of NSC content in needles decreased and then increased, and the percentage of NSC content in thick roots increased and then decreased. Seedling height, ground diameter, and biomass were greatest in the L3 treatment, and NSC content of thick roots was highest in all treatments. (2) The plasticity index of needle and fine root biomass was the highest, and there was a general positive correlation between seedling growth and NSC. Seedling height, ground diameter, stem biomass, needle soluble sugar, needle starch, fine root soluble sugar, and fine root starch were the important indices of shade adaptation, and the L3 treatment had the highest principal component values. In conclusion, P. yunnanensis seedlings will respond to the shade environment by changing the distribution of biomass and NSC in organs, and moderate shade was favorable for the regeneration and cultivation of P. yunnanensis seedlings in the understory, therefore, it is recommended that appropriate light penetration logging be carried out during the renewal of understory P. yunnanensis seedlings, and shade treatment be used during the cultivation of seedlings.