Metro Traction Power Supply System in the use of the 24-pulse rectifier unit , is composed of two 12-pulse rectifier unit connected in parallel. If two 12-pulse rectifier unit will generate a lot of job insecurity harmonics, a threat to the safe operation of the subway. Therefore, from the harmonic analysis of the rectifier unit rectifying characteristics, harmonic control for 24-pulse rectifier unit added three-level active filter. This paper focuses on topology and control algorithm of the three-level active filter to analysis and research. Finally, the combination of simulation and experiment shows that the active filter on the subway 24-pulse rectifier traction power supply system non-characteristic harmonic control has some compensation.