Plantations sequester atmospheric carbon dioxide and positively respond to climate change, but the carbon (C) sequestration capacity and the trade-off between plant and soil systems in plantations may vary significantly across a chronosequence. Masson pine (Pinus massoniana Lamb.) plantations were selected to investigate the variability of C stocks in 7-, 14-, and 30-year-old stands. The total ecosystem C stock increased with stand age from 14.82 to 19.21 Mg C. Carbon stocks increased with stand age in the plant system but decreased in the soil system, with the ratio of plant-to-soil C stocks increasing from 0.06 in the 7-year-old plantation to 0.70 in the 30-year-old plantation. Carbon stocks in the first 20 cm of the soil accounted for 44.60%, 43.01%, and 30.18% of the total ecosystem carbon stock in 7-, 14-, and 30-year-old plantations, respectively. The variation trends for the proportions of C stock in soil decreased with soil depth as a result of tree and root growth regardless of stand age. Most C was stored in the stems, which contributed 1.36%, 6.85%, and 29.57% of total ecosystem C stock across the chronosequence. Results of structural equation model indicated that the effect of plant system C stock on ecosystem C stock was far larger than soil system C stock, and saturated hydraulic conductivity (ks) and fractal dimension (D) could be the primary parameters affecting ecosystem C stocks according to redundancy analysis (Variance explained by the variables selected). In summary, the plant system increased biomass C stocks by regulating soil properties to meet their growth requirements, the growth of plants in turn changed the soil organic carbon (SOC) stock, then both regulated ecosystem carbon sequestration in Masson pine plantations.