An object occupies an enclosed region in the visual field, which defines its spatial extent. Humans display exquisite finesse in spatial extent perception. Recent series of human neuroimaging and monkey single-cell studies suggest the spatial representation encoded in the early visual cortex (EVC) as the neural substrate of spatial extent estimation. Guided by this EVC hypothesis on spatial extent estimation, we predicted that human estimation of spatial extents would reflect the topographic biases known to exist in spatial representation in EVC, the co-axial and radial biases. To test this prediction, we concurrently assessed those two spatial biases in both EVC and perception by probing the anisotropy of population receptive fields in EVC, on the one hand, and that of spatial extent estimation in human, on the other hand. To our surprise, we found a marked topographic mismatch between EVC and perceptual representations of oriented visual patterns, the radial bias in the former and the co-axial bias in the latter. Amid this topographic mismatch, the extent to which the anisotropy of spatial extents is modulated by stimulus orientation is correlated across individuals between EVC and perception. Our findings seem to require a revision of the current understanding of functional architecture in EVC and its contribution to visual perception: spatial representation in EVC (i) is governed by the radial bias but only weakly modulated by the co-axial bias, and (ii) do contribute to spatial extent perception, but in a limited way where additional neural mechanisms are called in to counteract the radial bias in EVC.