Penghu Harbor is a domestic commercial port for Taiwan's outlying islands, and it is a natural harbor. Located on the southwest coast of the main island of Penghu, it serves as the primary gateway for maritime transportation to and from the Penghu archipelago and is a major port for the importation of essential goods for the local residents.

1937-1939
The Japanese engaged in the construction of commercial and fishing port facilities in Magong (Makung), making Magong Harbor the primary port for foreign imports and exports during the Japanese colonial period in Penghu. After the relocation of the Nationalist government to Taiwan, Magong Harbor underwent continuous expansion, including the construction of piers and related port facilities.

1947
The Kaohsiung Harbor Bureau established the Magong Office in Penghu, officially designating Magong Harbor as a subsidiary port of Kaohsiung Harbor.

2014
The Ministry of Transportation, aiming for the development of the Penghu region, announced the integration of the port functions of Magong Harbor and another port, Longmen Jian Shan Harbor, consolidating them into the Penghu Domestic Commercial Port.