Model predictive torque control (MPTC) is a kind of powerful control scheme for high performance control of induction motor (IM) drives, which provides very quick dynamic response. However, MPTC suffers from tedious and time-consuming tuning work for the weighting factors, which is an obstacle for its application, especially in the multilevel converters. To solve this problem, this paper proposes a model predictive flux control (MPFC) system based on space vector modulation (SVM) for IM drive supplied by a three-level neutral-point-clamped (3L-NPC) inverter. By translating the references of torque and stator flux magnitude into an equivalent new stator flux vector reference, MPFC eliminates the use for weighting factors. Based on the principle of deadbeat control, the new stator flux vector reference is further transferred to a voltage vector reference, which is then synthesized by a SVM block. Finally, the suppression of neutral point potential fluctuation is also taken into account by tuning the duty cycles of redundant small voltage vectors. Experimental results are presented to validate the effectiveness of the proposed method.