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Increasing carbon stock is one of four strategic pillars to achieve net-zero carbon emission by 2050 as Taiwan’s government claimed in 2021. Soil, the major carbon pool of terrestrial ecosystems, is therefore regarded as the primary target on carbon sink. Soil organic carbon (SOC) is a key element which benefits soil processes and health. SOC accumulation contributes to climate change mitigation and adaptation, and food safety as well as the vision of the “4 per 1000 Initiative”. Several land utilities and soil management practices, such as organic farming, afforestation, cover cropping, residue incorporation, rotation and reduced tillage, have been reported to build-up SOC. However, the impacts of each practice are less understood under local conditions in Taiwan. To determine the carbon dynamics on the paddy rice farming systems, Taiwan Agricultural Research Institute (TARI) and Tainan District Agricultural Research and Extension Station (TNDAIS) established long-term research sites in 2006. All of the plots in trials were organic fertilizers free except for remixed plant residues into soil after harvest. Both location and rotation significantly affected the SOC contents in soils. The contents of SOC under Rice-peanut (lowland-upland) rotation was lower (0.3 %) than those under rice-rice (lowland-lowland) cultivation due to faster decomposition rate of soil organic matter under upland conditions. Organic farming can enhance the SOC accumulation as the results from Kaohsiung District Agricultural Research and Extension Station (KDAIS), which started organic farming at Chinan Branch Station in 1988. Continuous organic farming reinforced about 1.5% SOC in soils under the paddy rice-highland crop rotation system after 12 years compared with conventional management. Organic farming has been booming in recent years because local customers are concerned with food safety, food security and sustainable environment. We estimate that organic and eco-friendly rice paddy farming systems can contribute about 187.0 kt SOC in 2040. These results point out the critical role of organic farming of paddy rice on SOC accumulation, as Taiwan keeps going to approach the goal of the “4 per 1000 Initiative”.