Substituting synthetic fertilizers with solid organic fertilizers (e.g., solid manure and compost) contributes to mitigating climate change by increasing soil organic carbon stocks. However, net climate benefits of organic substitution (OS) remain unclear as organic inputs might increase emissions of nitrous oxide and methane, potent non-CO2 greenhouse gases (GHG) from croplands. Here we perform a meta-analysis of 1666 field paired ob-servations with a machine learning model to explore the net climate benefits of OS and its climate mitigation potential for China. We show that OS achieves net mitigation of over 4 Mg carbon dioxide equivalent (CO2-eq) ha-1 yr-1 on dryland soils by increasing soil organic carbon without affecting non-CO2 GHG of both nitrous oxide and methane when compared to synthetic fertilizer on a total nitrogen basis. Conversely, OS has limit net climate benefits on paddy soils because of the increased methane emissions that almost offsets the annual soil carbon benefits. The net climate benefits were mostly determined by the duration of OS (-25 % contributions), with limited long-term benefits but can be improved with optimal substitution ratio of organic N and type of organic fertilizers. We estimate that OS has technical potential to shift China's croplands from current a net carbon source of-300 Tg CO2-eq yr-1 to a small sink of 6 Tg CO2-eq yr-1, with the reduction potential equals to 2-3 % of total national emissions on a 20-year time span. Over 80 % of the mitigation potential lies in arable lands with neutral to alkaline pH, low soil organic carbon and temperate climate. These findings underscore the potential of OS for climate mitigation which requires alignment of targeted practices and cross-sectoral policies to guide China's OS implementation strategy.