Police claimed the three confessed to the attack which wounded 58 people, including foreign tourists.
Two bombs planted behind loudspeakers at the discotheque of the Riviera Hotel on Prachawiwat Road went off at about 4am, sending New Year revellers fleeing in panic.
Some ran to the parking lot behind the hotel to retrieve their motorcycles when a third bomb attached to a motorcycle exploded. Fire engulfed the motorcycles, damaging about 20 of them.
Later a similar bombing attack took place at the Marina Hotel on Charoenkhet Road.
A bomb went off in the discotheque on the second floor of the hotel, sending revellers running in panic. A second bomb then exploded in the hotel parking lot.
Police said 31 people were injured in the second hotel attack, two in serious condition.
Meanwhile, Narathiwat governor Karun Suppakitwilekakarn said the three suspects were Muhammad Saki Madeurae, 23, Sahae Saa, 24 and Assaroh Mayi, 29, all from Narathiwat.
The arrest of the three suspects came after police inspected security cameras at the hotels, Karun said. Karun said one suspect confessed that the group wanted to instigate chaos during the New Year holiday.
An initial investigation by police showed that the three suspects had criminal records for involvement in violence in the province's Sungai Kolok and Sungai Padi districts.