Palaeoclimate proxies reveal a significant precessional impact on the low-latitude hydrological cycle. Classical theory suggests that precession modulates the interhemisphere summer insolation difference and hence controls the meridional displacement of the Intertropical Convergence Zone (ITCZ). Accordingly, low-latitude precipitation variations are expected to be in phase (for the Northern Hemisphere) or anti-phase (for the Southern Hemisphere) with the Northern Hemisphere summer insolation. However, increasing numbers of proxies, particularly those that are absolutely dated, reveal that variations in terrestrial precipitation at different low latitudes follow distinct precession rhythms that are very often out of phase with hemispheric summer insolation. The mechanism underlying such spatial–temporal complexity remains elusive. In this study, we performed theoretical analysis, climate simulations, and synthesis of geological records to hypothesise that the low-latitude hydrological cycle is paced by shifting perihelion rather than by the hemispheric summer insolation. More specifically, precession of the Earth’s rotation axis shifts the season and latitude of perihelion. Here, the latitude of perihelion is introduced as the latitude of Earth’s subsolar point during perihelion, which is the location where the most intense solar radiation is concentrated. At the time of perihelion, intense solar radiation heats the land faster than the ocean due to differing thermal inertia. This thermodynamically moves the tropical convection from the ocean to the land, contributing to enhancing the terrestrial precipitation around the perihelion latitude. As the precessional phase changes, perihelion moves toward different latitudes, causing asynchronous maximums in terrestrial precipitation at different latitudes. Perihelion can occur in any season; therefore, the insolation in individual seasons is equally important in shaping the orbital-scale climate changes at low latitudes. This offers new insight into the Milankovitch theory, which highlights summer insolation’s role in shaping orbital-scale climate change.