A waterproof thermal management module for a portable electronic device that including a housing and a heat source is disclosed. The waterproof thermal management module includes a separated chamber, a heat absorber, a radiator, a heat pipe and a fan. The separated chamber is set inside the housing and has a first air channel and a second air channel, wherein the first and second air channels communicate with the outside of the housing. The heat absorber is set inside the housing for contacting the heat source. The radiator is set inside the separated chamber. The heat pipe extends from inside the housing through the wall of the separated chamber into the separated chamber and connects the heat absorber and the radiator. The cooling fan is set in the separated chamber.