The instrumental record reveals that tropical cyclone activity is sensitive to oceanic and atmospheric variability on inter-annual and decadal scales. However, our understanding of the influence of climate on tropical cyclone behaviour is restricted by the short historical record and the sparseness of prehistorical reconstructions, particularly in the western North Pacific, where coastal communities suffer loss of life and livelihood from typhoons annually. Here, to explore past regional typhoon dynamics, we reconstruct three millennia of deep tropical North Pacific cyclogenesis. Combined with existing records, our reconstruction demonstrates that low-baseline typhoon activity prior to 1350 CE was followed by an interval of frequent storms during the Little Ice Age. This pattern, concurrent with hydroclimate proxy variability, suggests a centennial-scale link between Pacific hydroclimate and tropical cyclone climatology. An ensemble of global climate models demonstrates a migration of the Pacific Walker circulation and variability in two Pacific climate modes during the Little Ice Age, which probably contributed to enhanced tropical cyclone activity in the tropical western North Pacific. In the next century, projected changes to the Pacific Walker circulation and expansion of the tropics will invert these Little Ice Age hydroclimate trends, potentially reducing typhoon activity in the deep tropical Pacific.