To explore the realization method and applicability of the flood probability forecast under the comprehensive influence of various uncertain factors, the study was carried out in Shiguanhe River Basin from 2003 to 2020, on the premise of quantifying the input of rainfall, model parameters and uncertainty degree of structure. The probabilistic flood forecasting is realized by fusing the uncertainty of every source based on the MCMC method, while the reliability and accuracy of the prediction results are evaluated based on the coverage ratio and the certainty coefficient, respectively. The results show that synthesizing the 5% to 95% confidence interval of the probabilistic flood forecasting method can predict the flood development process in a stable envelope and reduce the possibility of false alarm and missing alarm effectively. The result of mean value forecast is better than that of original single model forecast, which improves the reliability and reference value of flood forecast.