To better understand the influence of apical dominance on the ecological stoichiometry of C, N, and P in Helianthus tuberosus L., we removed the apical meristems of plants at different growth stages and measured the C, N, and P contents of different organs (root, stem, leaf, flower, and tuber), as well as the corresponding C:N, C:P, and N:P ratios. Removing the apical meristem had no effect on the C content of any of the organs but did affect the contents of N and P. The C content of the stems, tubers, and branches was improved by removing apical dominance, and the C content of the leaves was reduced expect the last removing apical dominance. Meanwhile, the N content of the roots, stems, and tubers was decreased, and the N content of the branches and flowers was increased, whereas the P content was only increased in the leaves and tubers. The C:N, C:P, and N:P ratios ranged from 24.15 to 153.75, from 118.87 to 2265.72, and from 2.46 to 24.05, respectively. The mean N:P (10.67) indicated that the growth of H. tuberosus was mainly limited by nitrogen availability.