Fischer–Tropsch synthesis (FTS) is used extensively in the gas-to-liquids (GTL) process to produce clean, high-quality low emission transportation fuels from synthesis gas. In order to gain a better understanding of the phase behavior of the produced wax–water mixtures at reaction conditions by accounting for confinement effects of either hydrophilic or hydrophobic characteristics and catalyst nanoparticles (NPs), one needs to closely examine the validity of incorporating coarse grained approaches in the context of FTS. The present study focuses on simulating by means of atomistic (AA) and coarse-grained (CG) molecular dynamics (MD; CGMD) simulations the n-octacosane (n-C₂₈)–water mixture inside graphene (G) and graphene oxide (GO) mesopores under low-temperature FTS conditions (473.15 K) with the inclusion of a Co NP. Graphene derivatives were selected as they are emerging catalyst support materials in the FTS reaction and allow for direct comparisons between the AA and CG methodologies. We also evaluated the presence of long-chain alcohols such as dodecan-1-ol at 7 wt % on the n-C₂₈–H₂O mixture phase behavior. The AA simulations involved the use of the united atom TraPPE (TraPPE-UA) force field for n-C₂₈ and the alcohols and the TIP4P/2005 force field for water, while the MARTINI force field was used for the CG description. With regard to the mixtures inside the G pore, both AA and CG simulation methods capture the phase separation of the mixture, with water molecules occupying the center of the pore and n-C₂₈ forming layers at the pore walls; inside GO, both methodologies show that water separates near the surface and the model wax lies at the pore center. Both AA and CG simulations accurately capture the n-C₂₈ and H₂O diffusivity as a function of the distance from the G and GO pore centers, respectively, being lower closer to the pore surface. Dodecan-1-ol is mostly located at the n-C₂₈–H₂O interface showing a higher preference toward the wax as a consequence of increased van der Waals intermolecular interactions, slightly reducing the mobility of water. The agreement between AA and CG MD simulations paved the way for novel CGMD simulations with DFT-derived parameters for Co, to study the n-C₂₈–H₂O behavior in its presence. Our results show that the Co NP does not affect phase separation of the n-C₂₈–H₂O mixture inside the pores; however, water at such high concentrations covers the Co NP surface extensively. Given the experimental difficulties in exploring the relevant mechanisms at this scale, our results showcase that CGMD using the MARTINI force field can be employed to study FTS-related processes at this level and are expected to open new pathways in the investigation of confined mixtures relevant to the FTS reaction in the presence of supported catalyst NPs.