In order to support UCLA’s development of the 3 cm Miniature Xenon Ion (MiXI) thruster, Cal Poly has a 3 cm thruster under development. This version, called MiXI Cal Poly Version 1 (MiXI-CPv1), is complete and has been utilized in vacuum chamber thermal validation testing. Testing on this version was used to check the validity of heat transfer simulations modeled in SolidWorks. Investigations of the 3 cm ion thruster configuration were intended to discover the driving factors affecting the thermal behavior of the discharge chamber and surrounding design space. Numerical simulations indicate that the heating of the samarium cobalt permanent magnets can be mitigated through the implementation of two proposed modifications. The first modification is to implement a 2% thoriated tungsten filament cathode. This design exhibited maximum permanent magnet temperatures of 325°C, twenty-five degrees below the maximum upper temperature of 350°C. Since some magnetic degaussing effects have been observed at temperatures above 300°C, the aforementioned solution can be combined with a thruster design modification to achieve a reduced permanent magnet temperature of 298°C. This modification would involve increase the anode wall thickness from approximately 0.7 mm to 2 mm below the permanent magnet ring, creating a stepped anode design. Additionally, less effective solutions were proposed and modeled and are presented for completeness.