In Macau, badly hit by a super typhoon previous year, authorities were much more prepared this time, ordering casinos to close late on Saturday night as the storm approached.
Mangkhut made landfall in the city of Taishan in Guangdong province at 5 p.m. local time, packing wind speeds of 162 km/h.
Parts of Hong Kong and Macau were severely flooded, though there were no immediate reports of any fatalities.
Authorities in southern China issued a red alert, the most severe warning, as the national meteorological center said the densely populated region would face a "severe test caused by wind and rain" and urged officials to prepare for possible disasters.
The workers used pikes and shovels to dig into the mud Monday morning, with the use of heavy equipment limited on the soaked ground.
Nearly all flights in and out of Hong Kong were cancelled.
Netizens in Hong Kong and mainland China have taken to social media to post videos of the widespread destruction caused by winds of more than 250kmh and waves over 12m high.
Hundreds of flights have been cancelled at Hong Kong International Airport and all high-speed rail services were also halted. The city of Shenzhen also cancelled all flights between Sunday and early Monday morning. Hainan Airlines canceled 234 flights in the cities of Haikou, Sanya, Guangzhou, Shenzhen and Zhuhai scheduled over the weekend.
Fifteen people were injured in the nearby gambling enclave of Macau, which closed casinos for the first time.
Yaonan Li, a resident in downtown Zhuhai, some 15 minutes outside Macau, told NPR the government was nervous about the typhoon but had learned its lesson from a typhoon a year ago.
In Macau's inner harbor district yesterday, the water level reached 1.5m and was expected to rise further.
Foreign aid has begun to trickle in for victims of the typhoon, with Australia pledging to provide more than US$572,000 worth of emergency supplies, such as sleeping mats, blankets and hygiene kits for up to 25,000 people.
The death toll in the Philippines, where the main island of Luzon was mauled with fierce winds and rain, rose to 65 overnight as rescuers pulled more bodies from a ill-prepared landslide in the mountain town of Itogon.
Families and relatives of miners carry their belongings as they evacuate following landslides which were triggered by Typhoon, burying an unknown number of miners and isolating the township in Itogon, Benguet province in the northern Philippines, on September 16, 2018.
At least 36 people, including the eight miners retrieved in Itogon, have died in typhoon-related incidents in the Philippines, mostly from landslides and collapsed houses.
Typhoon Mangkhut had the equivalent strength of a category 5 Atlantic hurricane when it made landfall on the Philippines on Saturday.
Philippines President Rodrigo Duterte traveled to Cagayan province Sunday to assess the damage and recovery efforts.
It earlier caused devastation in the Philippines , leaving at least 64 people dead and more than 40 more, mostly gold miners, trapped in a landslide.
Presidential adviser Francis Tolentino said about 87,000 people had been evacuated from high-risk areas and advised not to return home until the danger has passed.
"They thought they were really safe there", the mayor said.