In this work, the deformation of free interface during water entry and exit of a circular cylinder is investigated numerically by using the two-dimensional (2D) immersed boundary-multiphase lattice Boltzmann flux solver (IB-MLBFS). The fluid domain is discretized by finite volume discretization, and the flux on the grid interface is evaluated by lattice Boltzmann equations. Both the implicit velocity correction and the surface flux correction are implemented by using the immersed boundary-method to consider the fluid-structure interaction and the contact interface between the multiphase fluids and the structure. First, the water entry of a circular cylinder is simulated and the results are compared with the experiment, which considered the length-diameter ratio of the circular cylinder. The reliability of 2D simulation is verified and the deformation of the free interface is well investigated. Afterward, the water exit of a circular cylinder with constant velocity is simulated, which is less researched. In addition, the results show the advantage of present IB-MLBFS to some extent. Finally, the water exit and re-entry of a circular cylinder are presented, and the results present the complex deformation of the free interface and the dynamic response of the moving structure. Based on the numerical results, the free interface of the multiphase fluids is well captured, and the contact interface on the boundary of the moving structure is accurately presented by the IB-MLBFS.