In computational fluid dynamics (CFD), the physical domain is usually discretized by using mesh/grid, cells, nodes or particles generation. Although there are many advantages, these methods are required to have high computational storage/time cost, especially for solving the complex, deforming, and moving flows/bodies. Hence, we developed the vortex-in-cell (VIC) algorithm which is hybrid combination of grid-based and mesh-free method. VIC method, which was originally developed to simulate incompressible single-phase flows, becomes a very promising alternative for simulating complex flows. In addition, to simulate flows over deforming geometries, we utilized an immersed boundary method for enforcing the boundary condition. VIC interpolates the particle strength to an underlying mesh. VIC method has the advantage that the Poisson inversion can be accomplished by Fast Fourier Transform (FFT) techniques, this accelerates the computational time and provides accurate results. Here we consider an anguilliform swimming motion based on lateral displacement of the “backbone” which describes a complex, deforming, and moving body. “Flow over an Impulsively Started Circular Cylinder” problem are also simulated to validate the developed numerical method.