In the combustion applications of gas turbine engines, the twin fluid pneumatic atomizer plays a significant role. A pneumatic atomizer has been used to investigate the flow focusing (FF) and flow blurring (FB) modes of spray generation. To better understand the influence of operational and thermophysical parameters on internal two-phase flow mixing in a micro twin fluid atomizer, numerical simulations are run for four different air to liquid mass ratios with a constant water flow rate of 0.06 g/s. In addition, three different liquid fuels are studied for ALR of 1. ANSYS fluent was utilized to carrying out large eddy simulation (LES) with the volume of fluid (VoF) approach to track the interface precisely. FF mode was detected with an ALR of 0.25, while FB mode was observed with higher ALR ratios. The quantity of air entering the liquid tube increases with increasing ALR, indicating that the liquid jets break up internally upstream as a result of bifurcated air entering the liquid tube. For ALRs of 0.75 and 1, the quantitative values for penetration length are 0.35 mm and 0.475 mm, respectively. Thermophysical parameters also have an impact on the length of air penetration in the liquid tube. © 2023, The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.