Boats were recalled to shore across the Gulf of Thailand, while two key airports -- Koh Samui and Nakhon Si Thammarat -- were shut until Saturday, leaving tourists who remain on islands now cut off from the mainland.
"Ten thousand tourists are still on Koh Phangan," said Krikkrai Songthanee, district chief of the island which neighbours Samui and is famed for its full-moon party.
"But I talked to foreigners last night and they are not scared, they understand the situation," told AFP.
Pabuk, the first tropical storm in decades to strike during the peak holiday season, is expected to make landfall on Friday evening with the eye passing over Nakhon Si Thammarat further to the south.
"But all tourist islands in the Gulf of Thailand including Koh Samui, Koh Phangan, Koh Tao will be affected because Pabuk is huge," said Phuwieng Prakhammintara, head of the Thai Meteorological Department.
As it churns through the sea, Pabuk has picked up speed with 75-kilometre-an-hour (45 mile) winds stirring huge waves of up to five metres high (16 feet).
Social media videos showed oil rigs being battered by waves, and tankers navigating terrifying walls of water.
With rains lashing the entire south, the Meteorological Department warned coastal communities to expect "inshore surges" as winds whip up the sea.
Authorities have opened evacuation shelters for vulnerable communities across Thailand's southernmost provinces.
Pabuk is forecast to pass over the narrow neck of land between the Gulf of Thailand and into the Andaman Sea -- home to the tourist resorts of Phuket and the Similan National Park, a diving paradise.
Tens of thousands of tourists have already fled the southern zone.
"It's very empty... the beaches are deserted of tourists," Pui Suriwan, a Koh Phangan resident, told AFP.
On neighbouring Koh Tao, one of Southeast Asia's most popular dive spots, tourists and residents were bracing for a torrid 24 hours ahead.
"The weather is turning worse as the winds pick up, I've finished buying supplies... there's no gas anywhere on the island, 7/11 is already running out of things," a Spanish dive instructor told AFP.
"We're ready to bunker down."
Flights into Surat Thani, the gateway to Koh Samui, were nearly empty on Friday morning, a rare sight in Thailand's lucrative peak holiday season.
Thailand's economy is heavily reliant on tourism with the latest figures for 2017 showing the kingdom made nearly $60 billion from the sector.
Tourism was hit hard by a boat accident in Phuket in July last year when scores of Chinese tourists died as their overcrowded boat capsized in heavy seas.
Visitor numbers from China, Thailand's biggest market, slumped after the accident.