Background Deep space crewed missions require unique radiation shielding considerations. Due to mission duration and the heavy, high-energy nature of deep space radiation, the aluminum alloys that have historically been used for spacecrafts do not provide sufficient protection for crew members. Polymer-based nanocomposites have been proposed as potential radiation shielding materials for deep space applications; however, the high tunability of nanocomposites and the limited number of facilities able to produce representative radiation energies presents barriers to nanocomposite testing. Computational approaches may allow for preliminary investigation and discrimination of nanocomposite parameters like polymer and filler composition, loading percentage, and filler size and structure. Methods This work aims to investigate several modeling methods to perform radiation transport simulations for a nanocomposite, particularly with regards to modeling the filler nanostructure and the involved physics. Published experiments of a polydimethylsiloxane-carbon nanotube nanocomposite in 63 MeV and 105 MeV proton beams were digitally recreated in MCNP6.2 with three different nanocomposite structures. Additionally, several simulations were performed under various physics assumptions. The computationally determined water equivalent thicknesses are compared between modeling methods, as well as between the computational and the published experimental work. Results Nanostructure model complexity had no impact on the computed water equivalent thickness, with <1% difference between the three modeling methods. The inclusion of delta ray production and tracking physics produced a slight decrease in the computed water equivalent thickness and significantly increased the computational time for a single simulation by a factor of 35.7. Computationally determined water equivalent thicknesses are within 5% of published experimentally determined values. Conclusions Shielding capabilities of a polymer/carbon nanotube nanocomposite estimated using Monte Carlo radiation transport models agree well with published experimental results, even with a simplistic representation of the nanocomposite material. Radiation transport settings influenced the resulting water equivalent thickness as well as computational resource needs.