The study was to establish the fingerprints of Gannan navel orange from different growing areas and to make principal component analysis. The study carried out ultra performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry （UPLC-QTOF-MS） method to identify the common peaks of Gannan navel orange samples. The liquid-chromatographic separation conditions of this experiment were performed as followed： on a Agilent-C18 column （2.1 mm×100 mm， 1.8 μm）， using 0.1% formic acid aqueous solution（A）/ methanol （B） as the mobile phase with a flow rate of 0.3 mL/min through gradient elution， column kept at 35 ℃， and detection wavelength was set at 254 nm， mass spectrometry thorough scan in positive ion modes. The fingerprint of Gannan navel orange was established by all above chromatograms， and was researched the similarity of the fingerprint. The common peaks acquired from fingerprints were used principal component analysis. Results showed that there were twenty-one common peaks in the fingerprints of fourteen batches of Gannan navel orange samples， and the similarity of samples was above 0.90 with their characteristic fingerprint. Therefore， this method could be used to distinguish the non-Gannan navel orange sample. Through principal component analysis， four principal components were obtained， whose cumulative contribution of variance accounted to 85.75% of the total variance. The samples can be classified into four groups. Through the analysis of the positive ion mass spectra information and the relevant reports， 3 compounds of Common peak were identified. This method is accurate， reliable and well reproducible， and the established fingerprint combined with principal component analysis can be used for the identification of the navel orange and its origin.