We can grasp various features of the outside world using summary statistics efficiently. Among these statistics, variance is an index of information homogeneity or reliability. Previous research has shown that visual variance information in the context of spatial integration is encoded directly as a unique feature, and currently perceived variance can be distorted by that of the preceding stimuli. In this study, we focused on variance perception in temporal integration. We investigated whether any variance aftereffects occurred in visual size and auditory pitch. Furthermore, to examine the mechanism of cross-modal variance perception, we also investigated whether variance aftereffects occur between different modalities. Four experimental conditions (a combination of sensory modalities of adaptor and test: visual-to-visual, visual-to-auditory, auditory-to-auditory, and auditory-to-visual) were conducted. Participants observed a sequence of visual or auditory stimuli perturbed in size or pitch with certain variance and performed a variance classification task before and after the variance adaptation phase. We found that in visual size, within modality adaptation to small or large variance, resulted in a variance aftereffect, indicating that variance judgments are biased in the direction away from that of the adapting stimulus. In auditory pitch, within modality adaptation to small variance caused variance aftereffect. For cross-modal combinations, adaptation to small variance in visual size resulted in variance aftereffect. However, the effect was weak, and variance aftereffect did not occur in other conditions. These findings indicate that the variance information of sequentially presented stimuli is encoded independently in visual and auditory domains.