The persistent increase in carbon dioxide concentration in the atmosphere remains the main contributor to global climate change. This has prompted various researchers to design, develop and investigate materials to stabilize its growing threat. One of the best known methods is the biological approach of using microorganisms such as microalgae that have higher conversion efficiency as compared to terrestrial plants. Apparently, its full potential has not been achieved due to variations in several cultivation parameters such as temperature and salinity, which have not been well understood in the current experimental studies. The study is conducted in the atomic level to demonstrate the effects of temperature and salinity on the transport processes of carbon dioxide molecules coming from the flue gas to the microalgae lipid membranes using molecular dynamics. The transport process was described through the calculation of free energies of the carbon dioxide molecules across the membrane using the Cavity Insertion Widom method. The resulting free energy profile of the carbon dioxide molecule at different levels of temperature and salinity has shown no significant changes to its mobility in permeating inside the membrane despite changes in the lipid hydrocarbon chain structure. This suggests that microalgae are capable of absorbing carbon dioxide molecules at high temperature and salinity levels.