Previous neuroimaging studies based on electroencephalography (EEG) microstate analysis have identified abnormal neural electric activity in patients with psychiatric diseases. However, the microstate information in individuals with different degrees of fear of heights (FoH) remains unknown so far. The aim of the study was therefore to explore the changes of EEG microstate characteristics in different FoH individuals when exposed to high-altitude stimulated by virtual reality (VR). First, acrophobia questionnaire (AQ) before the experiment and 32-channel EEG signals under the virtual high-altitude exposure were collected from 69 subjects. Second, each subject was divided into one of three levels of FoH including no-FoH, mild or moderate FoH (m-FoH) and severe FoH (s-FoH) groups according to their AQ scores. Third, using microstate analysis, we transformed EEG data into sequences of characteristic topographic maps and computed EEG microstate features including microstate basic parameters, microstate sequences complexity and microstate energy. Finally, the extracted features as inputs were sent to train and test an support vector machine (SVM) for classifying different FoH groups. The results demonstrated that five types of microstates (labeled as A, B, C, D and F) were identified across all subjects, of which microstates A-D resembled the four typical microstate classes and microstate F was a non-canonical microstate. Significantly decreased occurrence, coverage and duration of microstate F and transition probabilities from other microstates to microstate F in m-FoH and s-FoH groups were observed compared to no-FoH group. It was also demonstrated that both m-FoH and s-FoH groups showed a notable reduction in sample entropy and Lempel-Ziv complexity. Moreover, energies of microstate D for m-FoH group and microstate B for s-FoH group in right parietal, parietooccipital and occipital regions exhibited prominent decreases as comparison to people without FoH. But, no significant differences were found between m-FoH and s-FoH groups. Additionally, the results indicated that AQ-anxiety scores were negatively correlated with microstate basic metrics as well as microstate energy. For classification, the performance of SVM reached a relatively high accuracy of 89 % for distinguishing no-FoH from m-FoH. In summary, the findings highlight the alterations of EEG microstates in people with fear of heights induced by virtual high-altitude, reflecting potentially underlying abnormalities in the allocation of neural assemblies. Therefore, the combination of EEG microstate analysis and VR may be a potential valuable approach for the diagnosis of fear of heights.