Various studies proved that the smoking quality of cigarettes are not merely decided by one or several kinds of chemical components, the aroma and flavour perceptions of a cigarette are the combined results from multi-components of cigarette smoke. The complexity of gas chromatograms of cigarette smoke needs suitable data treatment methods to establish relationship between smoke quality and smoke chemistry. Methods of data treatments such as chromatograms subtraction, pattern recognition based on principal components analysis (PCA), factor analysis and cluster analysis had been applied for the cigarette smoke evaluation. However the fingerprint total anomaly index (TAI) method has not been reported in this field. In this paper, the TAI method combined with high resolution capillary gas chromatographic analysis of cigarette smoke was used to quality evaluation of cigarette products. The allowances of all chromatographic peaks were determined by using their weight of peak areas that indicate the peak significance. The TAI represents the difference between two cigarette smoke fingerprint chromatograms, includes anomaly index of common, absent and excess chromatographic peaks. Finally, the TAI was successfully employed in the treatment of GC data for cigarette smoke and the examples were given. The chromatograms of twelve cigarettes brands including Virginia-type, British flue-cured type and American blended-type were collected and the TAI of every chromatogram was calculated with a Virginia-type cigarette as standard. The TAI method was compared with PCA and chromatograms subtraction methods, the results indicated that the TAI provides more useful information of the complicated GC data.