Budai Port has long been a vital trading hub, connecting Taiwan with Fuzhou and Xiamen since the Ming and Qing dynasties. Back then, the port bustled with vessels, with salt being its primary export.

In October 1947, the Taiwan Provincial Government established the Budai Port Office to manage and oversee port operations. However, after severe typhoons damaged the port’s infrastructure and disrupted maritime operations, the Budai Port Office was closed in December 1980.

In 1986, the Ministry of Transportation and Communications approved the passenger and cargo route between Budai Port and Penghu Port. With funding support from the Provincial Government for the construction of breakwaters and wharves, a 250-meter passenger and cargo wharf was completed in 1989, laying the foundation for Budai Port's operational development.

In 1993, the Chiayi County Government secured NT$990 million in subsidies from the Provincial Government. Starting in 1994, annual budget allocations were dedicated to expanding Budai Port's passenger and cargo facilities. By November 1997, the port had four and a half passenger and cargo wharves completed, supporting vessels for offshore island routes, round-island travel, and bulk and general cargo.

On October 28, 1998, the Executive Yuan designated Budai as a domestic commercial port. This decision was officially announced by the former Taiwan Provincial Government on November 11 of the same year, placing Taiwan International Ports Corporation in charge. A preparatory office was set up on November 15, 1998, and on June 1, 2000, the Budai Port Office was formally opened to manage the commercial port’s operations.