The invention relates to an energy transfer type power battery quick balancing system and a control method thereof. The invention relates to the battery voltage balancing system and further relates to the control method of battery pack quick balancing process, which solves the problem that a balanced battery single body and an energy storing element are impacted through pulse current by a currentbalancer in the prior art. The system comprises a power battery pack single body battery voltage and flying capacitor voltage detecting network, a current sensor and a signal modulating circuit, a single chip microcomputer, an electric power transfer channel, a first filter circuit, a two-way buck-boost converter, a second filter circuit and a flying capacitor. After starting to work, the system firstly detects the battery pack single body battery voltage, the flying capacitor voltage and the charging/discharging current; and if the dropout voltage between the highest voltage of the battery single body and the lowest voltage of the single body exceeds a set value, the balancing operation is started.