Objective:To investigate the pathway-specific correspondence between structural and functional changes resulting from focal subcortical stroke as well as their causal influence on clinical symptom.Methods:In this retrospective, cross-sectional study, we mainly focused on unilateral subcortical chronic stroke patients with moderate-severe motor impairment assessed by Fugl-Meyer Assessment (upper extremity), as well as healthy controls. All participants underwent both resting-state functional magnetic resonance imaging and diffusion tensor imaging. To parse the pathway-specific structure-function covariation, we performed association analyses between the fine-grained corticospinal tracts (CSTs) originating from 6 subareas of the sensorimotor cortex (SMC) and functional connectivity (FC) of the corresponding subarea, along with the refined corpus callosum (CC) sections and interhemispheric FC. A mediation analysis with FC as the mediator was used to further assess pathway-specific effects of structural damage on motor impairment.Results:Thirty-five patients (mean age 52.7 ± 10.2 years, 27 men) and forty-three healthy controls (mean age 56.2 ± 9.3 years, 21 men) were enrolled. Among the six CST tracts, we identified nine structurally and functionally covaried pathways, originating from the ipsilesional primary motor area (M1), dorsal premotor area (PMd), and primary somatosensory cortex (p < 0.05, corrected). Functional connectivity for the bilateral M1, PMd and ventral premotor cortex covaried with secondary degeneration of the corresponding CC sections (p < 0.05, corrected). Moreover, these covarying structures and functions were significantly correlated with the Fugl-Meyer assessment (upper extremity) scores (p < 0.05, uncorrected). In particular, FC between the ipsilesional PMd and contralesional cerebellum (β = −0.141, p < 0.05, CI = [-0.319, -0.015]) and interhemispheric FC of PMd (β = 0.169, p < 0.05, CI = [0.015, 0.391]) showed significant mediation effects in the prediction of motor impairment with structural damage of the CST and CC.Conclusions:This study reveals causal influence of structural and functional pathways on motor impairment after subcortical stroke and provides a promising way to investigate pathway-specific structure-function coupling. Clinically, our findings may offer a circuit-based evidence for PMd as a critical neuromodulation target in more impaired stroke patients and also suggest cerebellum as a potential target.