There will be one flight a week between HCMC and Kaohsiung from October 30 and four on the HCMC-Taichung route from November 18.
Visitors to Taiwan are no longer needed to furnish a negative Covid test result or make a medical declarations before boarding.
In recent years Vietnam has been among the biggest source of visitors for Taiwan, which has been enjoying a tourism boom.
In 2019, the year before the onset of Covid, it received over 777,000 Vietnamese tourists.
That year Vietnam saw a 30% rise in visitor numbers from Taiwan.
Vietnam reopened its borders and resumed pre-pandemic visa policies on March 15.