In recent decades, nanobubbles (NBs) have attracted great attentions of researchers in a number of fields, including aquaculture, water treatment, biomedical engineering and energy/power engineering. However, the fundamental understanding of these tiny bubbles through experimental techniques is very challenging. Dodecane, as a phase change material with a high boiling point, and isooctane, as an alternative fuel with high octane number and low volatility, have been researched and used in energy applications. In this work, the nucleation, coalescence and behaviour of formed NBs of carbon dioxide (CO2), oxygen (O2), nitrogen (N2), and hydrogen (H2) gases in dodecane and isooctane samples as well as their effects on the thermo-physical properties of the samples were investigated by means of molecular dynamics (MD) simulations. The weight fraction of the added gas and temperature were also investigated to understand their effects on the bubble dynamics and inherent properties. The results reveal that the addition of CO2 gas leads to the biggest drop in the viscosity of the dodecane by 20.47%, while the dispersion of oxygen gas in dodecane increases the viscosity. It is also found that samples containing NBs have higher specific heat capacity than samples without NBs and the highest specific heat capacity improvement can be obtained by dissolving hydrogen NBs. Furthermore, it is found that specific heat capacity of isooctane sample increases by increasing the weight fraction of dispersed gas. However, dodecane shows the opposite trend. By increasing the system temperature, the specific heat capacity of dodecane sample increases while isooctane sample again shows the opposite trend.