Soil carbon (C) sequestration by restoring degraded grasslands with adequate management practices offers significant opportunities for climate change mitigation while remaining highly uncertain. In this study, a combination of a biogeochemical model DayCent-CABBI and eddy covariance (EC) flux towers was applied to evaluate soil C sequestration potential (at a depth of 0–0.3 m) of management strategies in subtropical grasslands. DayCent-CABBI was calibrated for grasslands in northeast Australia using biomass and soil organic carbon (SOC) data from a long-term trial and then fine-tuned using EC flux tower data from seven sites in the region. The model was then validated with cumulative net ecosystem exchange, biomass, and SOC, resulting in root mean square errors of 1.16, 0.88, and 2.81 Mg C ha−1, respectively. The model was used to project long-term changes in SOC stocks under innovative management practices (time-controlled grazing and pasture legume incorporation), estimating soil C sequestration by 0.37–0.48 and 0.15–0.26 Mg C ha−1 year−1 toward 2050 with the respective practices. This study confirms the validity of the Measure, Model, and Verification (MMV) approach to estimate and project soil C sequestration for evaluating SOC methodologies by grassland management within a shorter period than soil sampling—measuring the baseline SOC, modeling the C dynamics with the calibrated DayCent-CABBI, and verifying the projected soil C sequestration with EC flux tower data.