Cirrus clouds in the tropical tropopause layer (TTL) and water vapor transported into the stratosphere have significant impacts on the global radiation budget and circulation patterns. Climate models, however, have large uncertainties in representing dehydration and cloud processes in the TTL, and thus their feedback on surface climate, prohibiting an accurate projection of future global and regional climate changes. Here we use unprecedented airborne measurements over the Pacific to reveal atmospheric waves as a strong modulator of ice clouds in the TTL. Wave-induced cold and/or cooling conditions are shown to exert a nearly ubiquitous influence on cirrus cloud occurrence at altitudes of 14–18 km, except when air was very recently influenced by convective hydration. We further observe that various vertical scales of cloud layers are associated with various vertical scales of waves, suggesting the importance of representing TTL waves in models.