A universal method was established for the systematically structural identification of nitrogen-containing compounds in crude oils. Pre-fractionation of the non-hydrocarbons in a crude oil sample into 7 fractions was performed by di-adsorption column chromatography using neutral aluminum oxide and silica gel; subsequent high-resolution separation of individual components was achieved by using capillary column gas chromatography, and compound types were detected by mass spectrometer. The two-dimensional data from the compounds in the fractions were further resolved by a chemometric method to obtained the deconvoluted chromatogram and mass spectrum of every compound, and then, the nitrogen-containing compounds were identified in combination with the retention indices. This method could relieve the difficulty of classical analysis in identifying those species with very low contents or incompletely separation, particularly in the cases where the authentic standards were not available for addition into the unknown samples in order to reveal what indeed existed in them. The structures of 168 nitrogen-containing compounds in a crude oil sample were determined by this method with satisfactory results.