Authorities in the heavily populated province of Guangdong have issued their highest warning level, a red alert.
Typhoon Mangkhut, also known as Ompong, also lashed Hong Kong with strong winds and heavy rain, as it crossed into the Chinese mainland.
The typhoon prompted storm surges as high as 10ft. and flooded ground-floor buildings in Shenzhen.
In the neighboring gambling enclave of Macau, all 42 casinos shut down for the first time in its history.
Bodies were still being pulled out of mudslides and rubble on the main island of Luzon in the Philippines, which bore the brunt of the super typhoon on the weekend with winds of more than 230 kilometers per hour.
State-run China Central Television (CCTV) reported the typhoon had killed two people in Guangdong.
Lily Chiu, a 60-year-old caregiver in Hong Kong, had stayed overnight at the nursing home where she worked to avoid commuting to an early shift when the storm hit. Mangkhut felled trees, tore scaffolding off buildings under construction and flooded some areas of Hong Kong with waist-high waters.
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The typhoon, dubbed the "King of Storms" by Chinese media, is expected to make landfall in Guangdong between the cities of Taishan and Yangjiang as early as 5 p.m. Sunday, weather officials say. The impact in the Philippines could be between 5 to 6 percent of its gross domestic product.
More than 2.4 million people were evacuated across China's southern Guangdong province in preparation for the deadly storm, AP reports.
More than 155,000 people remain in evacuation centres in the Philippines two days after the typhoon struck, said national police spokesman Benigno Durana.
"They thought they were really safe there", the mayor said.
Hong Kong's famed Victoria Harbor was hit with a storm surge of more than 3.9 meters (12.8 feet) above chart datum Sunday.
Tuguegarao airport in northern Luzon, a vital transportation hub, was damaged in the storm, forcing the cancellation of more than 100 local and worldwide flights, according to the Department of Transportation. Most of Hong Kong's public transport has been suspended. It also said more than 13,300 hectares of farmland had been damaged.
Philippine President Rodrigo Duterte, who visited the affected areas yesterday, pledged funds for the recovery efforts.
Last year, typhoon Hato, one of the strongest in recent years, pummeled the region, with Macau suffering wide damage and nine deaths, sparking criticism that authorities had not been well prepared.