A novel grid approach called Adaptive Mesh Refinement (AMR) using the Octree method for use within a kinetic Direct Simulation Monte Carlo Method (DSMC) and Particle in Cell (PIC) solver is described for an ion thruster application and results are compared with experimental findings. AMR is widely used in simulations characterized by multi-scale properties and serves as a powerful tool in terms of efficiency and flexibility. A single thruster configuration has been studied and it was found that the Charge Exchange (CEX) reactions have a major effect especially on the velocity field. Comparisons were made against experimental results in terms of energy distributions at two different axial locations. Finally, a three dimensional, three-thruster case was also simulated to see the effect on the plume and conditions in the domain which is hard to capture in experiments.