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Over three decades of in-situ observations illustrate that the Kelvin–Helmholtz (KH) instability driven by the sheared flow between the magnetosheath and magnetospheric plasma often occurs on the magnetopause of Earth and other planets under various interplanetary magnetic field (IMF) conditions. It has been well demonstrated that the KH instability plays an important role for energy, momentum, and mass transport during the solar-wind-magnetosphere coupling process. Particularly, the KH instability is an important mechanism to trigger secondary small scale (i.e., often kinetic-scale) physical processes, such as magnetic reconnection, kinetic Alfvén waves, ion-acoustic waves, and turbulence, providing the bridge for the coupling of cross scale physical processes. From the simulation perspective, to fully investigate the role of the KH instability on the cross-scale process requires a numerical modeling that can describe the physical scales from a few Earth radii to a few ion (even electron) inertial lengths in three dimensions, which is often computationally expensive. Thus, different simulation methods are required to explore physical processes on different length scales, and cross validate the physical processes which occur on the overlapping length scales. Test particle simulation provides such a bridge to connect the MHD scale to the kinetic scale. This study applies different test particle approaches and cross validates the different results against one another to investigate the behavior of different ion species (i.e., H+ and O+), which include particle distributions, mixing and heating. It shows that the ion transport rate is about 10 25  particles/s, and mixing diffusion coefficient is about 10 10  m 2  s −1 regardless of the ion species. Magnetic field lines change their topology via the magnetic reconnection process driven by the three-dimensional KH instability, connecting two flux tubes with different temperature, which eventually causes anisotropic temperature in the newly reconnected flux.