Variations in brain activity patterns reveal impairments of motor and cognitive functions in the human brain. Electroencephalogram (EEG) microstates embody brain activity patterns at a microscopic time scale. However, current microstate analysis method can only recognize less than 90% of EEG signals per subject, which severely limits the characterization of dynamic brain activity. As an application to early Parkinson's disease (PD), we propose an enhanced EEG microstate recognition framework based on deep neural networks, which yields recognition rates from 90% to 99%, as accompanied by a strong anti-artifact property. Additionally, gradient-weighted class activation mapping, as a visualization technique, is employed to locate the activated functional brain regions of each microstate class. We find that each microstate class corresponds to a particular activated brain region. Finally, based on the improved identification of microstate sequences, we explore the EEG microstate characteristics and their clinical associations. We show that the decreased occurrences of a particular microstate class reflect the degree of cognitive decline in early PD, and reduced transitions between certain microstates suggest injury in motor-related brain regions. The novel EEG microstate recognition framework paves the way to revealing more effective biomarkers for early PD.