Most numerical simulations of the flow in an internal mixer are based on the assumption that the internal mixer is totally filled with rubber compounds. However, in fact, the internal mixers are only partially filled with rubber compounds, thus posing many challenges for researchers in simulating the flow in the internal mixer. In this study, the volume of fluid method and the dynamic mesh technology of commercial CFD software FLUENT were used to simulate the flow of rubber compound in a partially filled internal mixer. To improve simulation accuracy, every 18 degrees in circumferential direction, we manually re‐meshed the calculated transient location of the rubber compound. Thus, we obtained the transient distribution of the rubber compound in the internal mixer as the rotors rotated. The simulation results showed that voids were mainly located behind the rotor blades, and there were material exchanges in the bridge regions between the two chambers. © 2015 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2015, 132, 42496.