The configuration of a single-phase three-level neutral point clamped (NPC) converter has been widely applied in high-speed railway electrical traction drive systems. This paper proposes a control and modulation scheme for the single-phase three-level NPC converter. Firstly, an active and reactive current decoupled control scheme in d-q synchronous frame is presented for single-phase three-level NPC converter to reduce the influence between the traction power supply fluctuating voltage and the traction drive system. Secondly, a new space vector PWM (SVPWM) scheme is provided to restrict the voltage step of the input port voltage within half of DC-link voltage. The proposed SVPWM algorithm is designed and analyzed in detail, including sector and basic voltage vector definition, sector identification, basic vector selection, the duty-time calculation and basic vector sequence design. Finally, the effectiveness and advantages of the proposed SVPWM scheme are confirmed by simulation and prototype experimental test.