Abstract: The probability analysis of precipitation encountering in the Yangtze River and Yellow River basins is of great significance for ensuring water security in China's South-to-North Water Diversion Project. Based on the reconstruction of precipitation data in different regions of the upper, middle, and lower reaches of the Yangtze River and Yellow River basin over the past 500 years, this paper uses the Copula function theory and the Multidimensional Variance Analysis Method to analyze the probability of precipitation encountering in different regions of the Yangtze River and Yellow River basins, with the uncertainty and main sources of the results illustrated. The results show that the probability of dryness-dryness encountering in different regions of the Yangtze River and Yellow River basins is relatively small, not exceeding 20%, and that the probability of dryness-dryness encountering in the upper, middle, and lower reaches of the basin does not exceed 10%. There is significant uncertainty in the calculation results of the encounter probability for the four combinations of wetness-wetness, dryness -dryness, wetness-dryness and dryness-wetness; compared with that in the upstream and midstream, the uncertainty in the downstream is generally less. The interaction between marginal distribution, the Copula function, and data sample length is the main source of uncertainty in the probability of precipitation encountering in the upper, middle, and lower reaches of the Yangtze River basin, with the Yellow River basin mainly affected by different sample sizes of data.