As a major port city in China, Zhuhai possesses 6 state-level 1 ports, 7 state-level 2 ports, among which Gongbei port is the second biggest land port in China. Thanks to Macao's steady economic growth and the laxing of traveling to Macao and Hong Kong, the exits and entries through Gongbei Immigrations exceeded 72 milliong person times during the first 11 months of 2007, with an average daily passenger flow of 230,000 person times, and the record passenger flow of 278,000 person times. Jiuzhou Port is the largest waterway passenger port in China. Zhuhai Port is a key hub harbour along the Chinese coastline with a capacity to accommodate an oil tanker up to 300,000 tons.

Gongbei Customs is a subordinate authority under direct control of the Customs General Administration of the People's Republic of China, and is responsible for supervision and control over all arrivals in and departures from the Customs territory within its jurisdiction in the cities of Zhuhai and Zhongshan.

Zhuhai also has a bonded zone of state-level.