More than 500 people were hurt when the storm raked across the island, including eight Japanese tourists whose bus was blown over. One remains in a critical condition.
Megi hit China with winds of around 120 kilometres (75 miles) an hour, dumping heavy rain, according to the official Xinhua news service.
Local media reports from the coastal province of Fujian said one man died after a flash flood tore through his home.
Schools were shuttered across the province and train services cancelled, Xinhua reported.
The main damage from the storm was in Taiwan, where schools and offices were shut for a second day after Megi left roads blocked by landslides and homes flooded.
The four deaths on the island included a man killed by falling scaffolding and a 17-year-old boy who drowned when his boat overturned.
Around 4,300 people remained in temporary shelters with more than 14,800 evacuated from their homes, according to Taiwan's Central Emergency Operation Centre.
At its peak, Megi knocked out power for close to 3.8 million households, the second worst on record after the outage caused by Typhoon Soudelor in August 2015.
A million households were still without power on Wednesday.
"Fallen trees and signboards brought down many power lines and electrical poles, leading to severe power outages across the island," Taiwan Power Company said.
Authorities were rushing to clear blocked roads Wednesday, including those leading to mountainous villages in the popular hot springs town of Wulai.
Wulai, one of the areas worst hit by Soudelor, had evacuated 200 residents ahead of the storm.
"The river swelled and flooded the old street, damaging basements of some homes," Shen Hui-kang, a spokesman at Wulai's district office, told AFP.
Mountainous areas across Taiwan have been lashed by torrential rains, with some parts of northeast Yilan county getting 1.3 metres (51 inches) since Monday.
Nearly 300 flights were either cancelled or delayed Wednesday and trains were still halted. They are set to resume later in the day.
Megi hit as parts of the island were still recovering from Typhoon Meranti earlier this month, the strongest storm on the island for 21 years.
Meranti, which left one dead in Taiwan before killing another 28 as it moved to eastern China, was followed closely by the smaller Typhoon Malakas.
