Miscanthus-dominated semi-natural grasslands in Japan appear to store considerable amounts of soil C. To estimate the long-term effect of Miscanthus vegetation on the accumulation of soil carbon by soil biota degradation in its native range, we measured total soil C from the surface to a 1.2 m depth along a catena toposequence in three annually burned grasslands in Japan: Kawatabi, Soni, and Aso. Soil C stock was estimated using a radiocarbon age and depth model, resulting in a net soil C accumulation rate in the soil. C4-plant contribution to soil C accumulation was further estimated by δ13C of soil C. The range of total soil C varied among the sites (i.e., Kawatabi: 379–638 Mg, Soni: 249–484, and Aso: 372–408 Mg C ha−1). Catena position was a significant factor at Kawatabi and Soni, where the toe slope soil C accumulation exceeded that of the summit. The soil C accumulation rate of the whole horizon in the grasslands, derived C mainly from C4 plant species, was 0.05 ± 0.02 (Average ± SE), 0.04 ± 0.00, and 0.24 ± 0.04 Mg C ha−1 yr−1 in Kawatabi, Soni, and Aso, respectively. Potential exists for long-term sequestration of C under M. sinensis, but the difference in the C accumulation rate can be influenced by the catena position and the amount of vegetation.