To ensure goal-directed behavior in daily life, the use of inhibitory control is of great importance. The aim of this study is to shed light on the underlying neuronal mechanisms of inhibitory control and the relevance of cytoarchitectonic integrity in it. We combine sophisticated EEG analysis techniques assessing directed communication between brain structures with measurements of neurofilaments as an index of cytoarchitectonic integrity. We show that an extensive theta band activity related neural network with fronto-temporal, parietal, and occipital brain regions is active during response inhibition. Importantly, cytoarchitectonic integrity as measured using neurofilaments modulates nonlinear directional connectivity, particularly when complex reconfiguration of perceptual and action mapping is required. The study thus shows an inter-relation between different levels of biological functioning-the level of cytoarchitectonic integrity and neurophysiological directed communication-for inhibitory control and emphasizes the role of nonlinear brain connectivity in cognitive control.