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Abstract Earth's orbital geometry exerts a profound influence on climate by regulating changes in incoming solar radiation. Superimposed on orbitally paced climate change, Pleistocene records reveal substantial millennial‐scale variability characterized by abrupt changes and rapid swings. However, the extent to which orbital forcing modulates the amplitude and timing of these millennial variations is unclear. Here we isolate the magnitude of millennial‐scale variability (MMV) in two well‐dated records, both linked to precession cycles (19,000‐ and 23,000‐year periodicity): composite Chinese speleothemδ¹⁸O, commonly interpreted as a proxy for Asian monsoon intensity, and atmospheric methane. At the millennial timescale (1,000–10,000 years), we find a fundamental decoupling wherein precession directly modulates the MMV of methane but not that of speleothemδ¹⁸O, which is shown to be strikingly similar to the MMV of Antarctic ice coreδ²H. One explanation is that the MMV of methane responds to changes in midlatitude to high‐latitude insolation, whereas speleothemδ¹⁸O is modulated by internal climate feedbacks.