Naxos was one of the major centres of the Cycladic culture. Around 3000BC, the main settlements appear to have been near Hora, on the hill of Kastro and at Grotta. The island was later colonised by a party from Karia, led by a son of Apollo named Naxos.

Naxos was one of the first islands to work in marble and in the Archaic period produced the lions of Delos and Kouroi statues of increadible size. Indeed, for a period, huge was beautiful on Naxos; in 523BC the tyrant Lygdamis declared he would make Naxos' buildings the highest and most glorious in all Greece, although only the massive lintel from the gate (Portara) of the Temple of Apollo remains on the islet of Palatia (in Naxos Town).

As with most of the islands Naxos declined in importance in the Classical age.

In Hellinistic times it was governed by Ptolemy of Egypt.