Police said there were two confirmed deaths in the Philippines as a result of the Super Typhoon.
Mangkhut crossed the northern part of the island of Luzon, where he made landfall in the darkness before dawn, tore off roofs, knocked down trees and cut off power.
The area is home to around 10 million people, many of whom live in flimsy wooden shelters.
When the powerful storm left the Southeast Asian archipelago and plunged into densely populated Hong Kong and southern China, the Philippines search teams began to inspect the provinces that suffered a direct blow.
"We believe that there has been a lot of damage," said Secretary of Social Welfare, Virginia Orogo, while thousands of evacuees took refuge in emergency shelters.
Mangkhut was packing sustained winds of 170 kilometers (105 miles) per hour and gusts of up to 260 kilometers per hour when leaving the Philippines.
An average of 20 typhoons and storms hit the Philippines each year, killing hundreds of people and leaving millions in near-perpetual poverty.
Thousands of people fled their homes in high-risk areas before the storm arrived due to large floods and the risk of landslides.
In Taiwan, a woman was dragged by strong waves caused by the typhoon, the government said.
"We are terrified"
Residents began flogging their roofs and collecting supplies days before the storm arrived.
"Among all the typhoons this year, this (Mangkhut) is the strongest," Hiroshi Ishihara, the forecaster of the Japan Meteorological Agency, told AFP.
"This is a violent typhoon, it has the strongest sustained wind (among typhoons this year)."
After bombing the Philippines, Mangkhut is expected to rush towards the densely populated south coast of China this weekend.
"They (the authorities) said that this typhoon is twice as strong as the last typhoon, that's why we are terrified," said Myrna Parallag, 53, after fleeing her home in the northern Philippines.
"We learned our lesson the last time, the water came to our roof," he said, referring to when his family left with a typhoon at his home in 2016.
The deadliest in the country in history is the Super Typhoon Haiyan, which left more than 7,350 people dead or missing in the center of the Philippines in November 2013.
Poor communities that depend on fishing are some of the most vulnerable to the fierce typhoon winds and storms that hit the coast.
"The rains will be strong and the winds will not be a joke … We may have a storm surge that could reach four floors," Michael Conag, spokesman for local civil defense authorities, told AFP.
As the storm heads towards China's southern coast, Cathay Pacific airline said it expects more than 400 flight cancellations in the next three days.
The Hong Kong government said Mangkhut will represent "a serious threat to the region" as many residents in the city and neighboring Macao stocked up on food and supplies.
The president of neighboring Taiwan, Tsai Ing-wen, pressured citizens to be ready.
"The typhoon is powerful and is not even expected to touch land in Taiwan, we must be well prepared and not … take it lightly," he wrote on Facebook.