<p>The human brain is an intricate network structurally organized across multiple scales. Multiscale structural architecture arises from complex biological mechanisms and provides the anatomical substrate for functional interactions. However, the extent to which the multiscale structural connectome constrains functional activity remains unclear. Here, we investigate the structure-function relationship by constructing an in vivo multiscale structural connectome that integrates white matter tractography, microstructural similarity, and cortico-cortical proximity. Multiscale structural connectome eigenmodes outperform conventional approximations of structural connectivity in capturing spontaneous and task-evoked functional activity. Moreover, multiscale structure-function decoupling reveals an organizational axis spanning from coupled unimodal sensory to decoupled transmodal association cortices, recapitulating microstructure and macroscale functional hierarchies. These decoupled patterns spatially align with opioid neurotransmitter receptors and mitochondrial succinate dehydrogenase, and colocalize with transcriptomic signatures enriched in synaptic structure and signaling regulation. Collectively, our findings highlight the pivotal role of multiscale structural wiring in shaping brain functional dynamics and provide novel neurobiological insights into the structure-function relationship.</p>