CO2 cooling systems are the wave of the future for industrial refrigeration. CO2 refrigeration systems are gaining traction in recent years which involves heat transfer between CO2 and the base fluid. The high viscosity of CO2 is of interest to the oil and gas industry in enhanced oil recovery and well-fracturing applications. A need arises to improve the thermal conductivity and viscosity of CO2 to increase the efficiency of these significant applications. Aggregation of nanoparticles is one of the crucial mechanisms to improve the thermal conductivity and viscosity of nanofluids. Since the aggregation morphology of nanoparticles is unclear so far, we have evaluated the stable configurations of the aggregation of nanoparticles by determining the potential energy of the different configurations system. In this paper, Green-Kubo formalism is used to calculate the mentioned thermo-physical properties of the different aggregated nanofluids. The nanofluid in this study consists of alumina (Al2O3) nanoparticles and CO2 as a base fluid. Results indicate that the enhancement in the thermal conductivity and viscosity of nanofluid is inversely proportional to the potential energy of the system. The results also mark that various morphologies of the aggregated nanoparticles have different enhancements of thermo-physical properties of the nanofluid. This study is conducive for the researchers to perceive the importance and influence of aggregation morphology of nanoparticles and their stability on the thermal conductivity and viscosity of nanofluid.