The Pacific cold tongue annual cycle in sea surface temperature is presumed to be driven by Earth’s axial tilt 1,2,3,4,5 (tilt effect), and thus its phasing should be fixed relative to the calendar. However, its phase and amplitude change dramatically and consistently under various configurations of orbital precession in several Earth System models. Here, we show that the cold tongue possesses another annual cycle driven by the variation in Earth–Sun distance (distance effect) from orbital eccentricity. As the two cycles possess slightly different periodicities 6, their interference results in a complex evolution of the net seasonality over a precession cycle. The amplitude from the distance effect increases linearly with eccentricity and is comparable to the amplitude from the tilt effect for the largest eccentricity values over the last million years (e value approximately 0.05) 7. Mechanistically, the distance effect on the cold tongue arises through a seasonal longitudinal shift in the Walker circulation and subsequent annual wind forcing on the tropical Pacific dynamic ocean–atmosphere system. The finding calls for reassessment of current understanding of the Pacific cold tongue annual cycle and re-evaluation of tropical Pacific palaeoclimate records for annual cycle phase changes.