Background The essential oil is one of the main active ingredients ofAmomum villosumLour. However, volatile compounds are easily lost during the drying, storage and even sample preparation procedure. Therefore, using fresh samples can obtain more accurately data for qualitative and comparative analysis. Methods In this study, the volatile compounds in different parts of freshA. villosumfrom different origins were systemic analyzed and compared by using cryogenic grinding combined HS-SPME-GC-MS for the first time. GC-MS analyses were performed on a 6890 Series GC instrument coupled to a 5973 N mass spectrometer. The volatile compounds were extracted by the SPME fiber (100 mu m PDMS). Analytes separation was achieved on a HP-5MS capillary column. The oven temperature was initially programmed at 70 degrees C, then raised 4 degrees C/min to reach 125 degrees C and then programmed at 0.5 degrees C/min to 133 degrees C, then at 6 degrees C/min to 170 degrees C and finally, at 20 degrees C/min to 280 degrees C held for 2 min. The temperatures of the injection port, ion source and transfer line were set at 250 degrees C, 230 degrees C and 280 degrees C, respectively. Results Forty-eight main compounds were identified in different parts of freshA. villosum. The most abundant components in fresh fruit samples were camphor (3.91%), bornyl acetate (10.53%), caryophyllene (8.70%), beta-bisabolene (11.50%), (E)-nerolidol (14.82%) and cubenol (10.04%). This is quite different with that of dried samples analyzed in our previous work. As different parts of the same plant, many common components with biological activities were detected in fruit and other parts. In principle components analysis (PCA) and hierarchical clustering analysis (HCA), four parts ofA. villosumwere divided into different groups clearly. Additionally, fruit and root samples also could be divided into two subgroups (HCA) in accordance with their regions. Conclusion The developed method was successfully used for qualitative and comparative analysis of volatile compounds in freshA. villosumsamples. Additionally, using fresh samples can obtain much more information which is helpful for their performance in the fields of functional foods, agriculture and biomedical industry. Furthermore, our research is helpful for comprehensive utilization and quality control ofA. villosum.