Penghu was developed quite early. According to historic records, people have inhabited here during the Shui and Tang dynasties. In the 6th year of Shuiyang of the Shui dynasty, Emperor Shuiyang used to send Chenlin to develop Penghu.
In the middle era of Emperor Shenchung of the Tang dynasty, Shi Chienwu settled in Penghu.

In the 7th year of Emperor Shiaochung of the South Sung, Penghu became a part of China domain. It was officially established in the 18th year of the Chih Yuan reign of the Yuan dynasty. It was the first officially established island of Taiwan Province.

In the early of the Ming dynasty, because people immigrated to Mainland China and the imperial government abolished the official control, Penghu was occupied by pirates. In the 2nd year of Tien Chi of the Ming dynasty, Dutch invaded Penghu, building up forts for coast defense. In the 4th year, Dutch troops were defeated and then invaded Tainan in Taiwan. 
Because of the failure of the Sino-Japanese War, the Ching dynasty was forced to sign the Treaty of Shimonoseki, ceding Taiwan and Penghu to Japan. In 1945, after defeating Japan, Penghu officially established a county government. In 1981, Makung Town promoted to be Makung City.

Archaeologists have found that there existed on Penghu's main island and other small islands as early as four to five thousand years ago "crude rope, striped pottery", "thin rope, striped pottery', and "simply decorated, red clay pottery" cultures, to name just a few, thereby verifying the origins of the cultural heritage of these islands.