The stand environment, tree growth, and carbon storage of plantations could be affected by thinning. Thus, to assess the dynamics of the forest ecosystem carbon pool, it is important to determine the changes of carbon storage in plantations after thinning.In 2013, the biomass, and carbon storage and allocation of Cunninghamia lanceolata plantations with different thinning intensities (i.e., H: 74%, M: 50%, and L: 34%) were studied using a biomass survey at the Experiment Center of Tropical Forestry of the Chinese Academy of Forestry. The results showed that the diameter at breast height (DBH) of H was significantly higher (P < 0.01) than M, L, and CK (0%), which increased by 13.65%, 20.74%, and 18.37%, respectively. There was no difference in the height of trees between the three thinning intensities; however, the height of trees in CK (0%) plots was higher than those in plots of the three thinning intensities, which increased by 6.64%, 15.73%, and 16.70%, for H, M, and L, respectively. The individual biomass with H was significantly higher (P < 0.01) than that for M, L, and CK. The carbon storage of the arbor layer in CK was significantly higher (P < 0.05) than that in the three thinning intensities, and the carbon storage in different organs was in the order: stem > branch > root > bark > leaf. There was no difference between the carbon storage of C. lanceolata plantation ecosystems with the three thinning intensities and CK plots. The arbor and soil layers were the main carbon pools, accounting for more than 97.62%.