Milankovitch forcing exerts a major control on climate that is recorded in the sedimentary rock record. However, its influence on hyperpycnal flow sedimentation is largely unknown. Hyperpycnites, sediments resulting from hyperpycnal flows, which are related to climate through flood frequency and magnitude, may be valuable tools for understanding aspects of Earth’s paleoclimate. Their origin and distinctive layering have been explained by various mechanisms, including frequency of river breaches, sudden increase in the global hydrological cycle, sea-level fluctuations, and variations in sediment supply. Their potential link to paleoclimate variations commonly remains unexplored in detail. Here we use cyclostratigraphic analysis combined with published high precision U-Pb dating to investigate the influence of Milankovitch forcing on their deposition. A continuous drill core of the ~125-million-year-old Early Cretaceous Laiyang Formation (eastern China) reveals well-defined cyclic hyperpycnal flow patterns. The radioisotopic dating and magnetostratigraphy constrains the formation’s average sedimentation rate, and links the observed cycles to precession, obliquity and mainly orbital eccentricity cycles. Orbital parameters most likely paced the delivery of the hyperpycnal flow sediments mainly by river- and delta-supplied currents from non-marine basin immediately; we conclude that Milankovitch cycles exerted a primary control on hyperpycnal flow sedimentation. Sediment accumulation rates determined from 400 kyr cycle age model show a trend of decreasing and then increasing throughout the Laiyang Formation, which was synchronized with the evolution of sedimentary environment controlled by tectonic activity. This study shows that orbitally-induced climate change can also acted as principle driver on deep-marine terrigenous sediment accumulation within a tectonically active basin.