Stand structure affects tree efficiency for a competitive use of resources and largely determines stand productivity and carbon stocks. Consequently, research on individual size and differentiation of stand structures is critical for improving monoculture-stand productivity and carbon stock. Here, we studied the effects of four thinning intensities (control: 0%, LIT: 20%, MIT: 30% and HIT: 40%) in an experimental plantation of Cryptomeria japonica var. sinensis, and assessed the individual differentiation characteristics, diameter class-frequency distribution, stand productivity and carbon stocks over 6 years. The results showed that the Gini coefficient decreased with increasing thinning intensity and stand age. Self-thinning of the C. japonica stands occurred even after thinning, it was relatively high when stand were 10-13 years old but did not occur in the 6th year after thinning in treatments T2 and T3. The mean diameter of each treatment increased with increasing stand age, and the normal distribution curve of diameter class frequency gradually shifted to the right, with small changes in the control treatment and the larger one in treatment T3. Thinning increased the large-diameter (DBH ≥ 26 cm) timber, especially in T2, T3 treatments. Stand volume and productivity varied with stand age, with the greatest change in stand volume observed in T3 followed by that in the control treatment. Stand productivity at different thinning intensities generally decreased and then increased with increasing stand age. Although the carbon stock of individual trees and stand increased with time, the individual trees appear the obviously increased trendy with increasing thinning intensity. The results provided important insights into the implications of designing thinning intensity and timing, and determining the tree-size class removal to meet specific management objectives.