Accumulating evidence suggested that the brain is highly dynamic, thus investigation of brain dynamics especially in brain connectivity would provide crucial information that stationary functional connectivity could miss. This study investigated temporal expressions of spatial modes within the default mode network (DMN), salience network (SN) and cognitive control network (CCN) using a reliable data-driven co-activation pattern (CAP) analysis. We found reduced number of CAPs, as well as transitions between different CAPs of the DMN and CCN, in patients with MDD. These results suggested reduced variability and flexibility of these two brain networks in the patients. By contrast, we also found increased number of CAPs of the SN in the patients, indicating enhanced variability of the SN in individuals with MDD. In addition, the patients were characterized by prominent activation of mPFC and insula. More importantly, we showed that our findings were robust and reproducible with another independent data set. Our findings suggest that functional connectivity in the patients may not be simply attenuated or potentiated, but just alternating faster or slower among more complex patterns. The aberrant temporal-spatial complexity of intrinsic fluctuations reflects functional diaschisis of resting-state networks as characteristic of patients with MDD.