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Around 3000 BC the first settlements were built on Naxos, which was the dominant center of the so-called Cycladic culture. The colonization of an island along the course of the Neolithic culture combination was required (water, agriculture, a reed field, hunting grounds and sufficiently close connection to other centers for exchange of goods that were missing). The island should be a minimum size. Naxos met these requirements. Naxos was also at the junction between the early corridors that connected to Anatolia. It was one of the first Greek islands where marble was worked. This was the best quality marble and it was also exported to the south Minoan Crete, where also on the east coast a large trading post was discovered.

Since archaeologists found the same kind of pots that were in use on Naxos, which may indicate a colonization further south. From around 2000 BC are everywhere around the Mediterranean fire layers were found. Also on Naxos where sites have been destroyed. After the disaster on Santorini, which took place somwhere between 1613 and 1615 BC (dated on the basis of olive wood that was found) the north-south link road to Crete disappeared. The fleets and ports were also destroyed after a tsunami of 28 meter high. The transport of iron from Attica was now organized by the Mycenaeans. They build the eastern Anatolia route further and 'competet' the Cretans away.

At the end of the Mycenaean period around 1000 BC Naxos was settled by Ionians from Attica, who also founded the city of Naxos Town and the surrounding fertile plains. Around 735 BC disadvantaged residents of Naxos, along with their companions of Chalcis (in Euboea), founded a colony of called Naxos in Sicily, at the foot of Mount Etna.

The island in the 7th and 6th centuries BC had a remarkable prosperous period, mainly under the tyranny of Lygdamis, and in that time there was a famous school established for artists (visual arts and crafts). Lygdamis, who himself belonged to the aristocracy, called on the people to revolt against the nobility, who originally owned all the land. The historian Herodotus called them "the fat". Then he seized power, supported by the tyrant Pisistratus (Athens) and Polycrates (of Samos), which he could count to his friends. Lygdamis ruled Naxos from ± 550 to 524 BC.

Like arch-rival Paros, with which it once was at war, Naxos was (and is) rich in quality marble. It is found on the surface across the island. It is therefore not surprising that here a local school of marble masons and sculptors developed. The people from Naxos liked to expose their wealth and skills: in crowded places, everywhere in Greece, they founded impressive monuments and buildings, such as the Stoa of Naxos, the famous Lion Terrace on the island of Delos, and the sphinx of Naxos in Delphi (first half of the 6th century BC.).

In 501 BC. Naxos supported the Ionian revolt and was punished by them in 490 by a Persian expedition lead by Datis. From this catastrophe the island would never recover. The Battles of Salamis and Plataea were fought on the side of the united Greeks. After that it was a rather recalcitrant member of the Athenian Empire: the fact that the aliance against the Persians had come under the hegemony of Athens not easily accepted by the people from Naxos. After a long siege they lost their independence and had to watch Athenians settle on their island. The Athenian admiral Chabrias defeated the Spartan fleet in the strait between Paros and Naxos.

In 376 BC Naxos joined in Naxos joined the Second Athenian Empire, and it was a member of the island federation, which successively was under Egyptian, Macedonian and Rhodian influence, until it finally was incorporated in the Roman Empire in 41 BC. In the first years of the Christian era the Cyclades became more and more depopulated: in the time of Strabo (19 AD.) only Naxos, Paros, Tinos and Andros were still important.

Then the history of the island quietly went into the Byzantine period, which left behind many traces in various large and small churches, scattered everywhere. In the 9th century, the Cyclades were attacked by the Saracens, who used Crete as a base. For Naxos better times arrived in 1207 when the Venetian nobleman Marco Sanudo founded the Duchy of Aegaen Sea and made Chora (Naxos) his capital. His descendants (and later the Crispi family) ruled the island until 1566: then came the Turks, who stayed until 1829.