The present invention relates to a hybrid battery module with voltage balancing unit, which comprises: a first cell set; a first programmable fuse; a first discharging switch; a first charging switch; a first analog front end circuit; a first thermister; a second cell set; a second programmable fuse; a second discharging switch; a second charging switch; a second analog front end circuit; a second thermister; a controller; and a voltage balancing unit; whereby the voltage of the first cell set and the second cell set can reach a balance state by the voltage balancing unit; and during the charging process, the first charging switch and the second charging switch will simultaneously be turned off when it meets a safety event; and during the discharging process, the first programmable fuse and the second programmable fuse will simultaneously be burned off when it meets a critical safety event so as to prevent cell from being burned; Furthermore, the present invention also provides a method for charging and discharging a hybrid battery module with a voltage balancing unit.