How does our brain resolve conflicts in sensory input to generate conscious perception? Using high-resolution 7T fMRI, we addressed this question by investigating column- and layer-specific activity in cortical and subcortical regions in humans during binocular rivalry. Results showed that eye-specific rivalry modulation arises from lateral inhibition between adjacent ocular dominance columns in the superficial layers of the primary visual cortex (V1), but not in the ocular layers of the lateral geniculate nucleus (LGN) of the thalamus. Furthermore, our data support an active role of feedback signals from the intraparietal sulcus (IPS) in biasing and synchronizing local competitions in V1 into perceptually coherent representations, even in the absence of awareness of eye-of-origin information. These findings revealed the mesoscale neural circuitry of perceptual conflict resolution in humans: local conflict in sensory input is resolved by inhibitory microcircuits in the early sensory cortex, while feedback signals from parietal attention network bias and integrate local competitions into a unified conscious perception.