Marine environment plays an important role in source-sink processes of carbon dioxide (CO₂), methane (CH₄), nitrous oxide (N₂O) and hydrogen (H₂). Head-space equilibrium, purge and trap and gas chromatography (GC) have been widely applied to measure their concentrations in seawater for decades. However, these methods were almost manual. Large uncertainty of air-sea gases flux is closely related to lack of easy available and used method. We developed an automated headspace gas sampling equipment, and modified a GC system equipped with FID, ECD and PDD detector. The headspace gas sampling equipment was assembled by solenoid valves, switch valves, peristaltic pump and electromagnetic relay, etc. It could be edited and controlled by the Chemstation software of GC. Thus the modified headspace GC system could run automatically. Precision, accuracy, repeatability and determine limitation of this method are improved significantly than historical reported methods. Moreover, the only thing the operator needs to do is switching seawater sample one by one, indicated the method was used friendly. Based on this self-developed method, dissolved CO₂, CH₄, N₂O and H₂ in China’s shelf seas have been measured since 2014. Results showed that the survey areas in China’s shelf seas were source of atmospheric CO₂, CH₄, N₂O and H₂. Currently, tens of articles were published and tow official standard guides were formulated in past years. In addition, this method has been adopted by the National Marine Environmental Monitoring Center and Ocean University of China.