A method for fast determination of the component in complex samples by using gas chromatography-mass spectrometry (GC-MS) was developed and used for quantitative analysis of phenanthrene in soils. In the method, window independent component analysis (WICA) was used for resolving the mass spectrum and non-negative immune algorithm (NNIA) was employed for obtaining the chromatographic profile. Therefore, spectral and chromatographic information of a specific component can be obtained from the measured GC-MS data of overlapping and high background. Six soil samples collected from different places were analyzed. The tedious pretreatments in preparing the samples and the elution in the separation were simplified for speeding up the analysis. Due to the complexity of the matrix, standard addition method was adopted for the final quantification. The applicability of the method was validated with a spiked sample and the results of the six samples are reasonable.