Communications between different brain systems are critical to support complex brain functions. Unlike generally high functional connectivity between brain regions from same system, functional connectivity between regions from different systems are more variable. In the present study, we examined whether the connectivity between different brain networks were modulated by other regions by using physiophysiological interaction (PPI) on resting-state functional magnetic resonance imaging data. Spatial independent component analysis was first conducted to identify the default mode network (DMN) and several task positive networks, including the salience, dorsal attention, left and right executive networks. PPI analysis was conducted between pairs of these networks to identify networks or regions that showed modulatory interactions with the two networks. Network-wise analysis revealed reciprocal modulatory interactions between the DMN, salience, and executive networks. Together with the anatomical properties of the salience network regions, the results suggest that the salience network may modulate the relationship between the DMN and executive networks. In addition, voxel-wise analysis demonstrated that the basal ganglia and thalamus positively interacted with the salience network and the dorsal attention network, and negatively interacted with the salience network and the DMN. The results demonstrated complex relationships among brain networks in resting-state, and suggested that between network communications of these networks may be modulated by some critical brain structures such as the salience network, basal ganglia, and thalamus.