Few studies of extreme precipitation have been conducted in Northeast China, particularly at multi-timescales. We aim to enhance the understanding of changes and variability in extreme precipitation over the past 54 years (1961–2014) in this region. We have investigated the potential relationship among extreme precipitation, climate and agricultural drought focusing on several timescales in this region. Thirteen extreme precipitation indices at seasonal, annual, and growing-period scales were estimated on the basis of daily precipitation data from 70 meteorological stations. The results indicate that all extreme precipitation indices that reflect the features of extreme wet events showed increasing trends in spring, and the trends of these indices were almost negative for the other timescales. Spatially, the frequency, duration and intensity of extreme wet events decreased gradually from south to north. The range of influence and the duration of extreme dry events increased continuously in Northeast China. In Northeast China, extreme precipitation was more easily influenced by the polar climate than the monsoon. Furthermore, correlation between the extreme precipitation indices and comprehensive crop failure ratios of agricultural drought disasters (C index) confirmed that agricultural drought was heavily influenced by precipitation anomalies in this area.