More than 2.45 million people have been evacuated in China's Guangdong province as Mangkhut made landfall at 5 p.m. local time, according to Chinese state media.
Xinhua reported that 18,327 emergency shelters had been activated, and that 632 tourism and 29,611 construction sites had been shut down.
Hong Kong's weather observatory issued its highest storm warning alert -- a signal T10 -- and the normally bustling city was all but shut down as transport was suspended and torrential rain flooded roads and buildings.
Airports in Shenzhen, a technology hub across the border from Hong Kong, and on the resort island of Hainan also canceled all flights, according to Chinese state media.
Mangkhut is now expected to move inland of western Guangdong. While the storm has weakened, a T8 warning was still in place into Sunday evening -- meaning that winds with speeds of about 63 kph were expected.
The Philippines remains the worst hit, with more than 250,000 people affected by the storm across the country -- around half of those seeking shelter in evacuation centers in the country's north.
When Mangkhut made landfall in the Philippines Saturday morning at 1:40 a.m. local time, the storm was already packing winds of up to 270 kph (165 mph).
While the death toll is currently 54, with 32 people injured and 42 more missing, this is likely to rise in the coming days as rescue teams work to locate 36 people believed to be buried beneath landslides in the Cordillera Administrative Region, in the north of Luzon island.
As of Saturday, the storm had caused 51 landslides in the north of the Philippines.
The most severe damage came in Luzon's north, a sparsely populated region that's considered the breadbasket of the Philippines, although areas as far away as Manila -- more than 340 km (200 miles) from the eye of the storm -- were hit with heavy rains that caused flooding in urban areas.
The country is no stranger to tropical cyclones -- more than 6,000 people died when Super Typhoon Yolanda hit the Philippines five years ago, the worst in a generation. That storm displaced nearly 4 million people.
Along the coast, the gambling enclave of Macau closed all its casinos, and all fishing boats from China's Guangdong province were called into port.
Hong Kong's famed Victoria Harbor was also hit with a storm surge of more than 3.9 meters (12.8 feet) above chart datum on Sunday. More than 550 flights at airports in Hong Kong, Shenzhen and Guangzhou were also canceled, according to Flightaware.com.
Hong Kong authorities had been warning residents to prepare for the storm for days, and on Saturday, grocery stores were packed with people stocking up on goods. Buildings across the city were either boarded up or had their windows taped in order to mitigate the damage of broken glass.
Other cities around the Pearl River Delta -- which includes Hong Kong, Guangzhou, Shenzhen, Zhuhai and Macau -- were also on high alert.
Mangkhut was still expected to bring heavy rain to Hong Kong, with flood warnings in place for low-lying areas.
CNN's Joshua Berlinger and Hilary Whiteman in Hong Kong, and Jo Shelley, Alexandra Field and Kathy Quiano in the Philippines, contributed to this report.