A power flow management method and a controller are provided. First, sensing voltage signals and sensing current signals between a power supplying module and a multilevel converter module are obtained. Positive sequence voltage signals, positive sequence current, negative voltage signals and negative current signals are generated according to the sensing voltage signals and the sensing current signals. Forward powers are calculated according to the positive sequence voltage signals, positive sequence current, negative voltage signals and negative current signals. DC voltage signals are obtained from the multilevel converter module, and feedback powers are calculated accordingly. A magnitude and a phase of a zero sequence voltage injection signal are determined according to the forward powers and the feedback powers. Accordingly, the generated zero sequence voltage injection signal is used to manage power flow effectively.