The research on brain functional mechanism and cognitive status based on brain network has the vital significance. According to a time–frequency method, partial directed coherence (PDC), for measuring directional interactions over time and frequency from scalp-recorded electroencephalogram (EEG) signals, this paper proposed dynamic PDC (dPDC) method to model the brain network for motor imagery. The parameters attributes (out-degree, in-degree, clustering coefficient and eccentricity) of effective network for 9 subjects were calculated based on dataset from BCI competitions IV in 2008, and then the interaction between different locations for the network character and significance of motor imagery was analyzed. The clustering coefficients for both groups were higher than those of the random network and the path length was close to that of random network. These experimental results show that the effective network has a small world property. The analysis of the network parameter attributes for the left and right hands verified that there was a significant difference on ROI2 (P = 0.007) and ROI3 (P = 0.002) regions for out-degree. The information flows of effective network based dPDC algorithm among different brain regions illustrated the active regions for motor imagery mainly located in fronto-central regions (ROI2 and ROI3) and parieto-occipital regions (ROI5 and ROI6). Therefore, the effective network based dPDC algorithm can be effective to reflect the change of imagery motor, and can be used as a practical index to research neural mechanisms.