The flywheel energy storage system (FESS) can operate in three modes: charging, standby, and discharging. The standby mode requires the FESS drive motor to work at high speed under no load and has the longest operating time. Therefore, reducing the standby losses is of great significance for further promoting the application of FESS. In the paper, a novel modulation technique based on hybrid space vector pulse width modulation (HSVPWM) is proposed to reduce the standby losses of the FESS. By the reasonable arrangement of the zero vectors and non-zero vectors, the proposed method can reduce the switching frequency and eliminate the dead time, which reduces the standby losses of the FESS effectively. The modeling, simulation, and analysis verify the effectiveness of this method in reducing the standby loss of the FESS.