The settlement's temple honoring the Chinese sea goddess Mazu, the deified form of the medieval Fujianese shamaness Lin Moniang, is usually accounted the oldest in all of Taiwan and Penghu. The town was originally named Makeng (Chinese: 媽宮; Pe̍h-ōe-jī: Má-keng; literally: "mother's palace") but was changed to Makō (馬公) during Japanese rule in 1920, and was the center of the Mako Guard District.
After 1945, the Wade-Giles romanization Makung was used. Taiwan officially adopted Hanyu Pinyin in 2009, leading to the romanization Magong.
The island's Mazu temple was erected in the late 16th or early 17th century. The city Magong'ao began to grow around 1887, during the Qing Empire's Guangxu Era.
Under Japanese rule, the settlement was renamed Makō and organized as a subprefecture of Hōko. The area was a major base of the Imperial Japanese Navy. It was an embarkation point for the invasion of the Philippines during the Second World War.
On 25 December 1981, Makung was upgraded from an urban township to be a county-controlled city.
Magong City contains 33 municipal villages (里 li):(Romanizations are in Hanyu Pinyin)
The city is powered up by the Hujing Power Plant located at Table Island.
It contains the domestic Magong Airport and Magong Harbor.