Recent neuroimaging studies have demonstrated that stimulation of acupuncture at motor-implicated acupoints modulates activities of brain areas relevant to the processing of motor functions. This study aims to investigate acupuncture-induced changes in effective connectivity among motor areas in hemiparetic stroke patients by using the multivariate Granger causal analysis. A total of 9 stable recovery stroke patients and 8 healthy controls were recruited and underwent three runs of fMRI scan: passive finger movements and resting state before and after manual acupuncture stimuli. Stroke patients showed significantly attenuated effective connectivity between cortical and subcortical areas during passive motor task, which indicates inefficient information transmissions between cortical and subcortical motor-related regions. Acupuncture at motor-implicated acupoints showed specific modulations of motor-related network in stroke patients relative to healthy control subjects. This specific modulation enhanced bidirectionally effective connectivity between the cerebellum and primary sensorimotor cortex in stroke patients, which may compensate for the attenuated effective connectivity between cortical and subcortical areas during passive motor task and, consequently, contribute to improvement of movement coordination and motor learning in subacute stroke patients. Our results suggested that further efficacy studies of acupuncture in motor recovery can focus on the improvement of movement coordination and motor learning during motor rehabilitation.