Hanoi came in second, followed by Phu Quoc, Da Nang and Nha Trang, Agoda said in a statement based on its booking data between January and June.
According to Agoda, Chinese travelers are drawn to Vietnam's major urban centers and island getaways.
Agoda's rankings also matched tourism statistics for the first half of the year.
Ho Chi Minh City received 3.85 million foreign visitors between January and June, up 44% year-on-year.
Mainland China remained the largest source of visitors to Vietnam during the January-June period, with 2.72 million arrivals, a 44% year-on-year increase.
Beach destinations like Phu Quoc, Nha Trang and Da Nang have been witnessing an influx of Chinese tourists.
A number of Asian celebrities like Chinese actor and martial artist Vincent Zhao, and Miss Hong Kong 2011 Rebecca Zhu recently visited Phu Quoc, further boosting its appeal.