This study aims to describe the double vortex motion via time-frequency analysis in cyclone separator, and propose a new cognition of the quantum characteristic of vortex energy transfer. A cylindrical cyclone separator with a large length-to-diameter ratio was designed to eliminate cone and dust hopper effects. Velocity was measured with a Phase Doppler Particle Analyzer (PDPA) and numerical simulations were performed via Reynolds stress model. The model was validated by comparison between numerical and experimental results. The results indicate that the total frequency distribution of fluctuating tangential velocity is neither a fixed value nor many decayed values in the cyclone separator. The total frequency has three specific values, according to which the flow in the cyclone separator can be divided to three regions (top, middle, and bottom). The flow performances differ in the three regions and have different spectrum forms. The fluid flow develops from single vortex motion dominated by a concentrated frequency to double vortex motion dominated by two concentrated frequencies. The energy is transferred from the high-frequency vortex to another low-frequency vortex. In this process, the motion frequency of vortex has self-preservation. The motion frequency of each vortex remains unchanged until the vortex disappears and the energy dissipates; the motion frequency in the whole cyclone is discontinuous, which encompasses the quantum characteristic.