Schizophrenia is a heterogeneous mental disorder with unknown etiology or pathological characteristics. Microstate analysis of the electroencephalogram (EEG) signal has shown significant potential value for clinical research. Importantly, significant changes in microstate-specific parameters have been extensively reported; however, these studies have ignored the information interactions within the microstate network in different stages of schizophrenia. Based on recent findings, since rich information about the functional organization of the brain can be revealed by functional connectivity dynamics, we use the first-order autoregressive model to construct the functional connectivity of intra- and intermicrostate networks to identify information interactions among microstate networks. We demonstrate that, beyond abnormal parameters, disrupted organization of the microstate networks plays a crucial role in different stages of the disease by 128-channel EEG data collected from individuals with first-episode schizophrenia, ultrahigh-risk, familial high-risk, and healthy controls. According to the characteristics of the microstates of patients at different stages, the parameters of microstate class A are reduced, those of class C are increased, and the transitions from intra- to intermicrostate functional connectivity are gradually disrupted. Furthermore, decreased integration of intermicrostate information might lead to cognitive deficits in individuals with schizophrenia and those in high-risk states. Taken together, these findings illustrate that the dynamic functional connectivity of intra- and intermicrostate networks captures more components of disease pathophysiology. Our work sheds new light on the characterization of dynamic functional brain networks based on EEG signals and provides a new interpretation of aberrant brain function in different stages of schizophrenia from the perspective of microstates.