Nanshan was largely a rural area before being rapidly developed since the late 1970s, with the exception of a few towns and villages. Nantou, the seat of Bao'an County for almost 1700 years was located within the district.
In September 1983, Nantou district was established as a county-level district. Less than a year later in August 1984, Shekou, which came to be known as Shekou subdistrict today, split off as a separate district from Nanshan. In September 1990,the two districts combined to form the present Nanshan District.
Nanshan experienced large sums of migrants from other parts of the country. Most of the original towns in the district had either been demolished to make way for developments or became what are to be known as urban villages.