A method based on microwave distillation (MD) and simultaneous headspace solid-phase microextraction (HS-SPME), coupled with gas chromatography-mass spectrometry (GC-MS), was developed for the rapid determination of essential oils in fruits of Alpinia oxyphylla Miq., a traditional Chinese medicine (TCM). HS-SPME conditions, including SPME fiber, desorption time, and microwave parameters (irradiation power and time), were optimized. The method simultaneously accomplishes the isolation, extraction and concentration of the essential oils. Compared to the conventional steam distillation (SD) method, which could only recover 35 compounds, MD-SPME led to the separation and identification of 53 compounds in the essential oils of Alpinia oxyphylla Miq. fruits. The intra-day and inter-day relative standard deviation (RSD) values of the MD-SPME-GC-MS method are all less than 8%, which shows that it has satisfactory precision. The MD-SPME-GC-MS method developed in this study is simple, rapid and solvent-free, and it shows promise for routine analysis of essential oils in fruits of Alpinia oxyphylla Miq. and, potentially, other TCMs.