Airports have been closed and flights cancelled in both southern China and Hong Kong.
The eye of Mangkhut, the Thai name for Southeast Asia's mangosteen fruit, skirted 100 kms (62 miles) south of Hong Kong but the former British colony was still caught in the typhoon's swirling bands of rain and gale-force winds.
Guangzhou, the capital and most populous city in Guangdong province, issued its highest typhoon emergency alert, according People's Daily, a state-run media outlet.
But officials in Hong Kong are still warning residents to be cautious.
Images have revealed collapsed building scaffolding and trees bending in the strong winds across Guangdong province.
Foam brought by high waves is seen washed ashore in Heng Fa Chuen, a residential area near the waterfront, during Typhoon Mangkhut in Hong Kong, China September 16, 2018.
The massive storm, considered this year's strongest, left key agricultural areas on Luzon island underwater as its fierce winds tore trees from the ground and rains unleashed dozens of landslides.
"Prepare for the worst", Hong Kong Security Minister John Lee Ka-chiu urged residents.
Cathay Pacific said earlier in a statement it's canceling all flights in and out of Hong Kong from Sunday 2:30 a.m.to Monday 4 a.m. Cathay Dragon also won't be flying. "It has the strongest sustained wind (among the typhoons of this year)".More news: The Ottawa Senators Trade Erik Karlsson To The San Jose Sharks
The typhoon is continuing on its path, with hundreds of thousands evacuating across China and Hong Kong in preparation. Macau suffered catastrophic flooding during Typhoon Hato past year, leading to accusations of corruption and incompetence at its meteorological office.
The damage in China is still unclear, but almost half a million people have reportedly been evacuated from the port and surrounding areas in Mangkhut's path.
"The landslides happened as some residents returned to their homes after the typhoon", disaster response coordinator Francis Tolentino said on DZMM Radio, adding that 5.7 million people had been affected and most were prepared.
The mayor expressed sadness that the villagers, many of them poor, had few options to survive in a region where big corporations have profited immensely from gold mines.
"It's very sad. I could hear villagers wailing in their homes near the site of the accident", Tacio said by phone.
The Philippines appeared to have been spared the high number of casualties many had feared.
A super typhoon made landfall in China's Guangdong on Sunday, the country's most populous province, after barrelling past Hong Kong and Macau and killing at least 29 people in the Philippines.
Two rescue workers were killed while trying to free people trapped in a landslide in the mountainous Cordillera region, said Ricardo Jalad, head of the nation's disaster agency.
The Philippines was just beginning to count the cost of the typhoon which hit northern Luzon on Saturday.