The Central Election Commission announced on Tuesday that a petition for a referendum had collected more than the required number of signatures.
The vote is likely to be held alongside regional elections on November 24th.
The name "Chinese Taipei" was decided by the International Olympic Committee and Taiwan in 1981 and accepted by China, which regards the island as part of its territory.
Beijing has criticized calls for the name to be changed.
In July, the East Asian Olympic Committee accepted China's request and decided to cancel the regional youth games that were to be held in Taiwan next year.
The decision to go ahead with the referendum is likely to draw more anger from Beijing.
