Supercontinent assembly and breakup can influence the rate and global extent to which insulated and relatively warm subcontinental mantle is mixed globally, potentially introducing lateral oceanic‐continental mantle temperature variations that regulate volcanic and weathering controls on Earth's long‐term carbon cycle for a few hundred million years. We propose that the relatively warm and unchanging climate of the Nuna supercontinental epoch (1.8–1.3 Ga) is characteristic of thorough mantle thermal mixing. By contrast, the extreme cooling‐warming climate variability of the Neoproterozoic Rodinia episode (1–0.63 Ga) and the more modest but similar climate change during the Mesozoic Pangea cycle (0.3–0.05 Ga) are characteristic features of the effects of subcontinental mantle thermal isolation with differing longevity. A tectonically modulated carbon cycle model coupled to a one‐dimensional energy balance climate model predicts the qualitative form of Mesozoic climate evolution expressed in tropical sea‐surface temperature and ice sheet proxy data. Applied to the Neoproterozoic, this supercontinental control can drive Earth into, as well as out of, a continuous or intermittently panglacial climate, consistent with aspects of proxy data for the Cryogenian‐Ediacaran period. The timing and magnitude of this cooling‐warming climate variability depends, however, on the detailed character of mantle thermal mixing, which is incompletely constrained. We show also that the predominant modes of chemical weathering and a tectonically paced abiotic methane production at mid‐ocean ridges can modulate the intensity of this climate change. For the Nuna epoch, the model predicts a relatively warm and ice‐free climate related to mantle dynamics potentially consistent with the intense anorogenic magmatism of this period.