A power conversion system with abnormal energy protection includes a plurality of DC input power sources (Vdc1-Vdcn), a plurality of DC power converters (11-1n), two output capacitors (41,42), and a protection circuit (20). An input side of each DC power converter (11-1n) is correspondingly coupled to one of the DC input power sources (Vdc1-Vdcn), and output sides of the DC power converters (11-1n) are coupled in parallel to each other to form a DC output bus (30). Two output capacitors (41,42) are coupled in series between a positive voltage end (Vb+) and a negative voltage end (Vb-) of the DC output bus (30). The protection circuit (20) is coupled between the DC input power sources (Vdc1-Vdcn) and the two output capacitors (41,42). When one of the two output capacitors (41,42) is abnormal, the protection circuit (20) decouples the DC input power sources (Vdc1-Vdcn) from the two output capacitors (41,42) in a shorted-circuit manner.