Neuroimaging studies have highlighted that intrinsic brain activity is modified to implement task demands. However, the relation between mental rotation and intrinsic brain activity remains unclear. To answer this question, we collected functional MRI (fMRI) data from 30 healthy participants in two mental rotation task periods (1st-task state, 2nd-task state) and two rest periods before (pre-task resting state) and after the task (post-task resting state) respectively. By combining the spatial independent component analysis (ICA) and voxel-wise functional connectivity strength (FCS), we identified FCS maps of 10 brain resting state networks (RSNs) within six different bands (i.e., 0–0.05, 0.05–0.1, 0.1–0.15, 0.15–0.2, 0.2–0.25, and 0.01–0.08 Hz) corresponding to the four states for each subject. The maximum uncertainty linear discriminant analysis (MLDA) method showed that the FCS within the low frequency bandwidth of 0.05–0.1 Hz could effectively classify the mental rotation task state from pre-/post-task resting states but failed to discriminate the pre- and post-task resting states. Discriminative FCSs were observed in the cognitive executive-control network (central executive and attention) and the imagery-based internal mental manipulation network (default mode, primary sensorimotor, and primary visual). Imagery manipulation is a stable mental element of mental rotation, and the involvement of executive control is dependent on the degree of task familiarity. Together, the present study provides evidence that mental rotation task specifically modifies intrinsic brain activity to complement cognitive demands, which provides further insight into the neural basis of mental rotation manipulation.