Local functional homogeneity of the human cortex indicates the boundaries between functionally heterogeneous regions and varies remarkably across the cortical mantle. It is unclear whether these variations have the neurobiological and structural basis. We employed structural and resting-state functional magnetic resonance imaging scans from 482 healthy subjects and computed the vertex-wise regional homogeneity of low-frequency fluctuations (2dReHo) and five measures of cortical morphology. We then used these metrics to examine regional variation, morphological association and functional covariance network of 2dReHo. Within the ventral visual stream, increases of 2dReHo reflect reduced complexity of information processing or functional hierarchies. Along the divisions of the prefrontal cortex and posteromedial cortex, the gradients of 2dReHo revealed the hierarchical organization within the two association areas, respectively. Individual differences in 2dReHo are associated with those of cortical morphology, and their whole-brain inter-regional covariation is organized into a functional covariance network, comprising five hierarchically organized modules with hubs of both primary sensory and high-order association areas. These highly reproducible observations suggest that local functional homogeneity has neurobiological relevance that is likely determined by anatomical, developmental and neurocognitive factors and should serve as a neuroimaging marker to investigate the human brain function.