The liquid carry-over (LCO) phenomenon brings about the performance deterioration of gas–liquid cyclone separator and an increase in pressure drop. However, the formation mechanism of the LCO and its manifestation in the separator cylinder and the overflow pipe have not been fully understood. This work investigated the flow process of the LCO by visual observation and quantitative measurement of the overflow liquid flow rate and liquid holdup. The transient gas–liquid flow feature in the overflow pipe and spatiotemporal relationship between the separator inlet and outlet were characterized by time-frequency analysis and wavelet coherence of liquid holdup, respectively. The results showed that the size of air core determines two kinds of sources of the LCO, including the surrounding liquid direct entry into the overflow pipe and the film short-circuit flow beneath the top wall of the separator. When the air core can continuously wrap up the overflow inlet, the film short-circuit flow became the primary source of the LCO, which was embodied in the significant reduction of the overflow liquid flow rate. Three flow patterns, namely, slug flow, churn flow, and annular flow, were classified in the overflow pipe. The inlet intermittent flow of the separator led to the distribution of churn flow expanding toward higher gas velocity, which was interpreted by flow pattern transition theory. The time-averaged overflow liquid holdup was well predicted by drift-flux model. The results are beneficial to the proposal of inhibition methods of the LCO and structure design of the separator.