The purpose of this present study is to address instability flowing characteristics and mechanism of the water-entry cavity created by a semi-closed cylinder. For this purpose, an experimental study and a numerical study of the water-entry of a semi-closed cylinder are carried out. According to the results of the experiments and comparison, the cavitating flows between the semi-closed cylinder water entry and the sealing cylinder water entry, and the fluctuation flow pattern form of the semi-closed cylinder cavitation is found around the body. The flow characteristics of the cavity shape are gained by analyzing the image data. A further insight into the mechanisms of perturbation to the flow structure and the cavity fluctuation by the air in the opening cell are studied based on the law of conservation of energy in water entry. According to the results of simulation and comparison with the cavity visualization of experiment, three instability flow phenomena of cavity are formed during the different stages of water-entry, i.e., flow separation destroyed, local flow transformed near cavity, and unique cavity shedding pattern. A further insight into the characteristics of the flow and the distribution of pressure and velocity during the stage of the cavity unstabilized flow is gained. Finally, the formation mechanism of the cavity unstabilized flow is studied based on the boundary layer theory and Helmhotz vortex theory. The obtained results show that the water poured into the cell of cylinder after the opening end has impacted free surface causes the internal air to compress and expand, and as a consequence of these effects, periodic disturbances of flow structure occur around the cavity, then the cavity presents an identical periodic wave flow with air piston motion and the flow stability of cavity is destroyed. At the eve of impacting, the opening end approaches the free surface, which leads to the inflow velocity attenuation rapidly and the pressure increasing in the cell, which creates an initial pressure higher than ambient pressure. Because of the high pressure, air efflux from the cell forms a gas jet injected into the cavity for the first air expansion stage, then the detaching flow is destroyed and the cavity extension diameter is enlarged. The flow in the gas-liquid mixing domain of cavity is seen as an approximate boundary layer flow pattern where favorable pressure gradient on the upwind side and adverse pressure gradient on the lee side appear alternately. As this flow pattern, re-entrant flow acting on the trough of wave cavitation results in the fact that the laminar-turbulent transition is weakened in the trough field and the local gas-liquid mixing domain is thickened to be involved in unstabilized structure as cloud cavitation. The wave cavity presents a partial and multiple shedding pattern occurring at the trough positions in sequence. There is no mutual interference between shedding cavity and the main cavity. Following the cavity shedding, vortex shedding is formed. The vorticity concentrates on the inside of shedding cavity, and the pressure and velocity present a coherent structure.