It said there could be storm surges of up to seven metres (23ft) in coastal areas and that heavy rains could spark landslides and flash floods.
On Guam, a USA territory, residents woke up on Tuesday to flooded streets, downed trees and widespread power outages after Mangkhut passed through overnight.
"As Mangkhut has a large circulation with intense winds, it will pose considerable threat to the coast of Guangdong", according to the Hong Kong Observatory.
An advisory from the JTWC on Tuesday said Mangkhut was packing winds of up to 250 kilometers per hour (kph) near the center and gustiness of up to 306 kph.
Shoppers were stocking up on fruits and vegetables, as well as fish and meat, with many stores selling out their wares earlier than usual, according to the South China Morning Post.
Even so, Guy said will come "dangerously close to clipping the country", causing heavy rain and flooding in the island's north, where local authorities are preparing relief goods and security forces have been put on alert.
Luzon was devastated by Super Typhoon Haima - known as Lawin locally - in 2016, with 14,000 houses destroyed and 50,000 homes damaged, according to CNN Philippines.
"I'm stressing that this one is very different".
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Schools and offices are being closed and farmers are racing to save crops.
Office of Civil Defense chief Ricardo Jalad said other northern provinces will also start evacuating residents from low-lying areas on Thursday.
The strongest typhoon to hit the Philippines this year is threatening the farmlands in Northern Luzon just before the rice and corn harvest.
President Rodrigo Duterte cancelled his Thursday plan to board a navy ship in Bataan in central Luzon to conduct a missile test.
Although there are still uncertainties about its trajectory, it is expected that Mangkhut will bring adverse weather to the regions of Macau, Hong Kong and the coastal cities of southern China.
With winds that may gust up to 240km/h, Mangkhut is expected to be more powerful than the Super Typhoon Wanda that resulted in heavy casualties in 1962 and the Super Typhoon Hato, which triggered the highest level typhoon warning signal previous year.
Typhoon Haiyan left more than 7,300 people dead or missing and displaced over five million in the central Philippines in 2013.
Meanwhile, the US east coast braces as Hurricane Florence barrels towards the Carolinas, expected to make landfall late September 14 or early September 15.