Changes in sea ice extent and polynya size and productivity associated with climate conditions in the Ross Sea region have an important role on the ecological responses of Adélie penguins ( Pygoscelis adeliae ). Nevertheless, there have been few studies that elaborate on the effects of atmospheric and oceanic circulation on their populations. Here, we reconstructed the population dynamics of Adélie penguins on Beaufort Island during the past 350 years using various alternative geochemical indices and Generalized Additive Models (GAMs). We explored the effects of atmospheric-ocean circulation patterns, including the El Niño-Southern Oscillation (ENSO), the Southern Annular Mode (SAM), and the Amundsen Sea Low (ASL), on the population ecology of penguins. The results indicated that their population on the island has been growing with fluctuations since ~1650 AD, and there were three significant increases, corresponding to 1650–1750, 1825–1900 and after 1950 AD. It was revealed that climate warming in this region was not a necessary factor for penguin population growth, since their populations maintained an increasing trend during the Little Ice Age (LIA) when relatively colder climate conditions prevailed. The present results indicated that atmospheric-ocean circulation patterns likely impose prominent influences on the historical change of penguin populations on Beaufort Island. • Historical penguin population was reconstructed by Generalized Additive Models. • Sea ice extent, polynya and temperature affect the penguin population directly. • Atmospheric-ocean circulation patterns may play a key role on penguins' ecology. • Warming in the Ross Sea region is not mandatory for larger penguin population.