The flavor fingerprint of Tricholoma matsutake Singer was developed and volatile compounds were investigated by HS-GC-IMS fingerprinting combining with PCA. A total of 25 typical target compounds were identified. The differences of flavor compounds in pileus and stipe of Tricholoma matsutake Singer from different areas were observed. After drying, the concentration of C8 compounds, including 3-octanone, 3-octanol, 1-octen-3-one and 1-octanol, decreased, while the concentration of methanol and 1-pentanol increased. Subsequently, PCA was performed based on the signal intensity of the identified violate compounds, and the results clearly showed that the samples in a relatively independent space would be well distinguished. Combining the signal intensity of the identified violate compounds by HS-GC-IMS and PCA, the samples from different portions of Tricholoma matsutake Singer and different areas were distinguished. The results showed that the flavor fingerprint of Tricholoma matsutake Singer were established by HS-GC-IMS and PCA based on the identified volatile compounds.