The South China Sea is an important part of China’s territory, and it has a great strategic significance for China. In order to ensure the reliability and availability of the data from the island weather stations, this paper analyzes the error messages that are generated by the original quality control system, and in order to reduce the number of false checks for the regional automatic stations on the South China Sea, a method is developed, which can check the data difference between two stations on the same island, and the spatial consistency check method is improved. By using the new method to check the data of the regional automatic stations on the South China Sea from September 2015 to July 2016, the removed false check messages accounts for 717% of the original false check messages. The accuracy of error detection is greatly improved.