To strengthen scientific management and sharing of greenhouse gas data obtained from atmospheric background stations in China, it is important to ensure the standardization of observations and establish the data treatment and quality control procedure so as to maintain consistency in atmospheric carbon dioxide (CO2) and methane (CH4) measurements from different background stations. An automated gas chromatographic system (Hewlett Packard 5890GC employing flame ionization detection) for in situ measurements of atmospheric CO2 and CH4 has been developed since 1994 at the China Global Atmosphere Watch Baseline Observatory at Mt. Waliguan, in Qinhai. In this study, processing and quality control flow of CO2 and CH4 data acquired by HP ChemStation are discussed in detail, including raw data acquisition, data merge, time series inspection, operator flag, principal investigator flag, and the comparison of the GC measurement with the flask method. Atmosphere CO2 and CH4 mixing ratios were separated as background and non-background data using a robust local regression method, approximately 72% and 44% observed values had been filtered as background data for CO2 and CH4, respectively. Comparison of the CO1 and CH, in situ data to the flask sampling data were in good agreement, the relative deviations are within +/- 0.5% for CO2 and for CH4. The data has been assimilated into global database (Globalview-CO2, Globalview-CH4), submitted to the World Data Centre for Greenhouse Gases (WDCGG), and applied to World Meteorological Organization (WMO) Greenhouse Gas Bulletin and assessment reports of the United Nations Intergovernmental Panel on Climate Change (IPCC).