Focal damage due to stroke causes widespread abnormal changes in brain function and hemispheric asymmetry. In this study, functional near‐infrared spectroscopy (fNIRS) was used to collect resting‐state hemoglobin data from 85 patients with subacute stroke and 26 healthy controls, to comparatively analyze the characteristics of lateralization after stroke in terms of cortical activity, functional networks, and hemodynamic lags. Higher intensity of motor cortical activity, lower hemispheric autonomy, and more abnormal hemodynamic leads or lags were found in the affected hemisphere. Lateralization metrics of the three aspects were all associated with the Fugl‐Meyer score. The results of this study prove that three lateralization metrics may provide clinical reference for stroke rehabilitation. Meanwhile, the present study piloted the use of resting‐state fNIRS for analyzing hemodynamic lag, demonstrating the potential of fNIRS to assess hemodynamic abnormalities in addition to the study of cortical neurological function after stroke.