<p>In the context of global climate change, enhancing the carbon sequestration potential of forest ecosystems through thinning practices is crucial. This study assessed the effects of five thinning intensities on carbon storage in various layers of forest ecosystems in young-aged, middle-aged, and near-mature <i>Larix principis-rupprechtii</i> Mayr plantations. The soil physicochemical properties, nutrient content, and enzymatic activities were analyzed to reveal the above mechanisms. Additionally, the variation of arbor carbon storage across different diameter at breast height (DBH) classes were analyzed over time by measuring at various intervals before and after thinning during three stand stages. While arbor carbon storage decreased with increasing thinning in middle-aged and near-mature forests, the loss of carbon storage decreased over time. The net change of arbor carbon storage in the large DBH class in thinned plots was higher than in control plots across all stand stages, but notable increases in the middle DBH class were only observed in young-aged forests under low-intensity thinning (15–20%). From 2014 to 2019, the growth rate of arbor carbon storage under low-intensity thinning (15–20%) surpassed that of the control. Thinning enhanced litter, soil, and total ecosystem carbon storage, displaying a rough “N” shaped pattern as thinning intensity increased. Total potassium (TK) was positively correlated with arbor carbon storage across all stand stages, whereas polyphenol oxidase (PPO) activity was significant only in middle-aged and near-mature forests. Each stand stage showed a significant positive correlation between carbon storage and both the carbon-to-nitrogen (C/N) ratio in the litter layer and urease (URE) activity in the soil layer. In conclusion, although 35% thinning intensity showed a beneficial effect on total ecosystem carbon storage, low-intensity thinning (15–20%) was more conducive to arbor carbon growth.</p>