The history of Budai Port can be traced back to the Ming and Qing dynasties. Serving as a trading port between Taiwan and mainland China's Fuzhou and Xiamen, budai port had heavy traffic flow and with salt being the primary export product.

The Taiwan Provincial Government established the Budai Office in October 1947 to oversee the operation and management of the port. However, shipping operations was wound down due to damage of the wharf facilities caused by typhoon. Budai Port Office was ordered to be disbanded in December 1980.

In 1986, the Ministry of Transportation and Communications (MOTC) approved the Budai-Penghu passenger/cargo shipping route and received subsidies from the provincial government to construct breakwaters and wharves. The passenger and cargo wharf, measuring 250 meters, was completed in 1989, laying the foundation for the development of Budai Port's operations.

In 1993, the Chiayi County Government received a subsidy of 990 million NT dollars from the provincial government. And since 1994, budgets were allocated annually to carry out the expansion project of the Budai Port passenger and cargo wharf. By November 1997, 4.5 passenger and cargo wharves were completed, catering to the docking needs of ships transporting goods and passengers to and from outlying islands and along the coast.

On October 28th 1998, the Executive Yuan approved Budai Port as a domestic commercial port. Then the former Taiwan Provincial Government announced Budai Port as a domestic commercial port on November 11th of the same year. And the Harbour Bureau was designated as its competent authority. On November 15th of the same year, the Budai Port Preparatory Office was established. Until June 1st of 2000, the Budai Office was officially approved to establish to oversee the management and operation of the commercial port and related matters.