Abstract. Rice paddies are a major anthropogenic source of the atmospheric methane. However, because of the high spatial heterogeneity, making accurate estimations of the methane emission from rice paddies is still a big challenge, even with complicated models. Data scarcity is one of the substantial causes of the uncertainties in estimating the methane emissions on regional scales. In the present study, we discussed how data scarcity affected the uncertainties in model estimations of rice paddy methane emissions, from county/provincial scale up to national scale. The uncertainties in methane emissions from the rice paddies of China was calculated with a local-scale model and the Monte Carlo simulation. The data scarcities in five of the most sensitive model variables, field irrigation, organic matter application, soil properties, rice variety and production were included in the analysis. The result showed that in each individual county, the within-cell standard deviation of methane flux, as calculated via Monte Carlo methods, was 13.5–89.3% of the statistical mean. After spatial aggregation, the national total methane emissions were estimated at 6.44–7.32 Tg, depending on the base scale of the modeling and the reliability of the input data. And with the given data availability, the overall aggregated standard deviation was 16.3% of the total emissions, ranging from 18.3–28.0% for early, late and middle rice ecosystems. The 95% confidence interval of the estimation was 4.5–8.7 Tg by assuming a gamma distribution. Improving the data availability of the model input variables is expected to reduce the uncertainties significantly, especially of those factors with high model sensitivities.