In the late 1930s, the site of today's Zhuhai Jinwan Airport was first developed into an airfield known as Sanzao Airport, constructed by Japanese forces in 1938 during the occupation of parts of South China, where it served as a military air base in the Second World War.

After Japan's defeat in 1945, the airfield fell into long-term disuse, functioning only intermittently for limited military or general aviation purposes. In 1948, the runway at Sanzao Airport was destroyed by the Chinese Nationalist government. By 1949, the abandoned airfield had fallen into disuse and was repurposed by local fishermen as a place for drying fish and grain.

On 18 December 1989, the State Council and the Central Military Commission approved Zhuhai's request to use the Air Force's Sanzao Air Base for civil aviation operations. At that time, the airport operated under a 'military–civil dual‑use' arrangement, meaning that the local government was permitted to conduct civil aviation activities on what remained an active military facility.

A major transformation began in 1992, when Zhuhai authorities decided to rebuild the abandoned Sanzao airfield into a modern civil aviation airport. This redevelopment culminated in the opening of the new facility— then named Zhuhai Sanzao Airport.

When large‑scale construction of Zhuhai Airport began in 1993, it was built to China's highest 4E‑class standard, with a planned runway length of 4,000 meters. At that time, no airport in the country had ever constructed a runway of this length.

At the time of its opening in 1995, the airport featured a 4,000‑metre runway and one of the most advanced sets of navigation and terminal facilities in China, with a terminal building (now Terminal 1) that ranked among the largest of its kind in the country.

One year later in 1996, the first China International Aviation & Aerospace Exhibition was hosted at the airport.

Between 1996 and 2006, Zhuhai Sanzao Airport entered a prolonged downturn, struggling to attract passengers due to the dense concentration of major airports in the Pearl River Delta (Guangzhou, Shenzhen, Hong Kong, and Macau), as well as inconvenient ground transportation links. As a result, traffic volumes fell far short of expectations, and the airport faced severe financial losses and mounting debt. There were numerous reports that the airport was going bankrupt due to funding and financial problems, which the authorities repeatedly denied.

In October 2006, the Zhuhai municipal government and the Airport Authority Hong Kong established the joint venture "Zhuhai–Hong Kong Airport Management Co., Ltd.," placing the airport under the management of the Hong Kong Airport Authority. This arrangement marked the first time a mainland Chinese airport had been operated under Hong Kong's management model.

After adopting the Hong Kong airport management model, Zhuhai Jinwan Airport has entered a period of rapid growth and expansion. In 2013, the airport was officially renamed "Zhuhai Jinwan Airport," marking a new phase in its development. Benefiting from Hong Kong Airport Authority's management experience and the surge in domestic air‑travel demand, passenger throughput rose steadily year after year.

In 2018, the airport handled more than 11.22 million passengers, placing it firmly among China's "ten‑million‑class" airports.

With the continued rise of the Zhuhai Airshow and deeper integration within the Greater Bay Area, the airport launched its Terminal 2 expansion project, and by 2024 it achieved a historic record of nearly 13 million passengers—its highest annual traffic to date.