Pinus yunnanensis has high economic and ecological value. The survival of P. yunnanensis has been greatly affected by global warming. This study examines the response of P. yunnanensis seedlings to drought stress and their recovery following rewatering, focusing on growth metrics and C:N:P stoichiometry. This experiment included the four following treatments: CK (water content was 90% ± 5%); LS (water content was 75% ± 5%); MS (water content was 60% ± 5%); and SS (water content was 45% ± 5%). This experiment also included a continuous drought period of 30 days followed by 7 days of rewatering. This study found that drought limited the growth of seedlings, and seedlings could recover rapidly from the damage caused by LS and MS treatments after rewatering, and the recovery of seedlings was greater following LS and MS treatments than following SS. After the drought, the C content in the leaves and stems of P. yunnanensis seedlings could recover to CK levels after rewatering. The N content of each organ and the P content of fine roots of P. yunnanensis seedlings showed an upward trend after rewatering. In summary, the growth of P. yunnanensis seedlings was significantly affected by drought stress, and the recovery mechanism of rewatering varied depending on the degree of drought. Combining the phenotypic plasticity index and principal component analysis, the stem biomass, thin root biomass, root/shoot ratio, leaf C:P, leaf N:P, leaf P, stem C:P, thin root N, thin root P, coarse root N, coarse root P, and coarse root C were the most important indexes for adaptation to drought and rewatering.