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Converging evidence has found that the perceived visual size illusions are heritable, raising the possibility that visual size illusions might be predicted by intrinsic brain activity without external stimuli. Here we measured resting-state brain activity and 2 classic visual size illusions (i.e. the Ebbinghaus and the Ponzo illusions) in succession, and conducted spectral dynamic causal modeling analysis among relevant cortical regions. Results revealed that forward connection from right V1 to superior parietal lobule (SPL) was predictive of the Ebbinghaus illusion, and self-connection in the right SPL predicted the Ponzo illusion. Moreover, disruption of intrinsic activity in the right SPL by repetitive transcranial magnetic stimulation (TMS) temporally increased the Ebbinghaus rather than the Ponzo illusion. These findings provide a better mechanistic understanding of visual size illusions by showing the causal and distinct contributions of right parietal cortex to them, and suggest that spontaneous fluctuations in intrinsic brain activity are relevant to individual difference in behavior.