The sustainability of agricultural lands is at risk owing to intensive farming practices coupled with undesirable activities like deforestation, soil erosion, and overgrazing, which serve as the drivers of the reduction in soil organic carbon (SOC). To support the ever-growing global population with food and nutrition, the indiscriminate application of inorganic chemical fertilizers not only exacerbates the ecological balance but also increases the discharge of greenhouse gases like carbon dioxide (CO2), nitrous oxide (N2O), and methane (CH4) from the soil to the open atmosphere. This results in the reduction in the potential of the soils to produce healthy and nutritious crops for mankind. Carbon sequestration proves to be a climate-resilient strategy for capturing and storing soil carbon stocks, thereby enhancing the physicochemical and biological properties of soil and emerging as a carbon-neutral country in the near future. Hence, proper estimation of carbon sequestration potential and its prediction in the future in various cropping systems is vital to maintaining the sustainability of the soil ecosystem. Biophysical models like APSIM, DNDC, DSSAT, ROTH-C, EPIC, CENTURY, and SWAT-C are some of the often-used models in organic carbon simulation in long-term field experiments. By considering drivers like climate, soil properties, agronomic practices, and plant physiology, they can accurately simulate carbon fluxes, the dynamics of soil organic matter (SOM), and the impacts of land use changes on carbon sequestration. Moreover, these models enable scenario analysis, facilitating the assessment of various management strategies and their potential impacts on carbon sequestration, thus aiding in the development of sustainable agricultural practices aimed at mitigating climate change. Thus, a clear understanding of these soil carbon simulation models is crucial in modern-day agriculture for upscaling the degraded lands and preserving the degrading ones.