A total of 65-year rainfall data collected from 30 meteorological stations in Jilin Province during 1951 to 2015 was analysed by sliding average method, anomaly analysis method and Mann-Kendall mutation test, combined with MapInfo, ArcGIS software and R language drawing tool. The interdecadal, interannual and annual variation characteristics of rainfall in flood season in Jilin Province were used to reveal the multi-time scale characteristics of rainfall variation and the periodic variation and mutation points of rainfall sequences at different time scales. The results show that: 1) the interdecadal and interannual rainfall in Jilin Province shows a trend of fluctuating downward, especially in the 21st century, the decline in rainfall is more significant, and the sudden change points of annual precipitation occur in 1983 and 1992; 2) the monthly rainfall in flood season shows a significant downward trend, all but a small decline in June; 3) the rainfall during the flood season is mainly concentrated in July and August, accounting for 65% of the total rainfall during the flood season. The average proportion in September is the lowest, only 13%. In addition, the proportion of rainfall in June in the whole flood season has an increasing trend, that is, the rainfall in flood season is ahead of schedule; 4) the average rainfall intensity of each month in flood season shows an upward trend, and the decreasing rate of rainfall days is greater than that of rainfall.