The pressure gradient in the dual volute radial turbocharger turbines is the primary source of the vortices’ formation in rotor passages. The effects of the upstream non-uniform flow conditions on the development of secondary flows are not well known. In this study, the effect of highly skewed and non-uniform mass flow on the secondary vortices in different admission cases in a dual entry turbine was investigated using CFD modeling. The results agree well with the experiment, and show that increasing the inequality of the pressure between the entries leads to a reduction in the turbine’s performance. Some useful energy dissipates due to mixing the flows of the entries. Isolating the rotor sectors in the tongues region was applied with the purpose of limiting the mixing. Also, the vortices’ behavior in the rotor passages with different surface pressure ratios for the passage sides were investigated for both equal and partial admission. The surface pressure of the airfoil pressure side was more effective on the tip and trailing edge vortex than the suction side, while the leading-edge root vortex did not change by any variation in the surface pressure ratio. The vortices’ center location shifted with the pressure variation, and consequently, by decreasing the pressure level, the center of the tip vorticity turned to the upstream sections, and the leading-edge root vortex center moved closer to the pressure side.