Recent studies have demonstrated that the numerosity of visually presented dot arrays is represented in low-level visual cortex extremely early in latency. However, whether or not such an early neural signature reflects the perceptual representation of numerosity remains unknown. Alternatively, such a signature may indicate the raw sensory representation of the dot-array stimulus before becoming the perceived representation of numerosity. Here, we addressed this question by using the connectedness illusion, whereby arrays with pairwise connected dots are perceived to be less numerous compared with arrays containing isolated dots. Using EEG and fMRI in two independent experiments, we measured neural responses to dot-array stimuli comprising 16 or 32 dots, either isolated or pairwise connected. The effect of connectedness, which reflects the segmentation of the visual stimulus into perceptual units, was observed in the neural activity after 150 msec post stimulus onset in the EEG experiment and in area V3 in the fMRI experiment using a multivariate pattern analysis. In contrast, earlier neural activity before 100 msec and in area V2 was strictly modulated by numerosity regardless of connectedness, suggesting that this early activity reflects the sensory representation of a dot array before perceptual segmentation. Our findings thus demonstrate that the neural representation for numerosity in early visual cortex is not sufficient for visual number perception and suggest that the perceptual encoding of numerosity occurs at or after the segmentation process that takes place later in area V3.