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. 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. A three dimensional, three-thruster case was also simulated to see the effect on the plume and on the corresponding mesh structure when there is no axial or radial symmetry present. Finally, a parallel computing framework is introduced in order to extend studies to more computationally extensive cases and decrease the simulation times significantly.