In railway traction applications, due to the limitation of switching frequency and the attempt to fully utilize the DC-link voltage, the traction inverters usually work in six-step (or quasi-square-wave) mode under heavy load or high frequency condition. Meanwhile, DC-link voltage fluctuation, stemming from a common single-phase grid-side power supply, has a great impact on the drive system. To maintain high performance under fluctuating DC-link voltage condition is of practical significance. In this paper, a DC-link-fluctuation-resistant control scheme in six-step mode featuring DC-link fluctuation prediction and reference flux tracking is proposed. It uses a repetitive predictor to acquire future DC-link voltage pattern and accordingly plan the switching instance to track the flux references. Simulation has been conducted and high steady state and dynamic performances are proved.