Meteorological disasters are the result of the interaction of multiple factors and multiple systems. In order to improve the accuracy of prediction, it is necessary not only to consider the characteristics and cycles of each subsystem, but also to study the interaction of all systems. Based on the summer precipitation data and 130 circulation indexes of 34 national meteorological observation stations in Chongqing from 1961 to 2010, the prediction model of Chongqing summer precipitation was established based on the decision tree and the stochastic forest algorithm based on machine learning, and the prediction test of 2011–2018 was carried out independently by the model. Compared with the results of the single-factor prediction model, the trend consistency rate increased by 37.5% and 12.5% respectively. In addition, when using the random forest model to predict summer precipitation in Chongqing from 2014 to 2018, the 5-year average Ps, Cc and PC scores were 84.6, 0.27 and 67.1, respectively, which were significantly improved compared with 72.4, −0.12 and 52.9 of the current climate forecasting methods, and the forecast quality of the random forest was relatively stable. The multi-system collaborative impact model based on decision tree and random forest algorithm can achieve high accuracy and stability. Thus, this method can not only be an effective means for the diagnosis and prediction of climate causes, but also has a good theoretical and practical value for the prediction of extreme disasters.