With the development of Micro LEDs, the fluidic self-assembly (FSA) process has gained increasing attention recently. However, due to the high requirements of mass transfer processes for transfer rate, alignment accuracy, bonding strength, and reliability, the fluid selection of FSA still faces challenges. In this study, a fluid system named the PA-EC-TPO system with good application in the FSA process was proposed. To study the internal mechanism of the system, five PA-EC-TPO systems were designed, modeled, and simulated, using molecular dynamics (MD), tuning with different contents of PA and EC. The models were then calibrated with an error rate of 5% for density. On this basis, MD simulation results of CED, Eint, and AverageNumbonds were further extracted. The results showed that the strength of the PA-EC-TPO system was regulated by both the van der Waal term and electrostatic term, in which the proportion of the former was 2 to 3 times that of the latter, which proved the stability of the system decreased significantly with the increase of temperature. Finally, viscosity measurement and infrared spectroscopy were carried out to further verify the simulation results. It was clearly shown that the stability of the PA5-EC5-TPO system reached the optimum at 298K, which was applicable in the FSA process. In summary, this study proposed and analyzed fluid systems with MD simulation methods, which provided an internal mechanism for future FSA research.