The method for the determination of 5 kinds of trace heavy metal elements (Cu, As, Hg, Cd and Pb) in Fructus Aurantii by inductively coupled plasma-mass (ICP-MS) with HNO3-H2O2 microwave digestion was established. The recoveries of the elements detected were in the range of 85%～109% and the relative standard deviations (RSD) was in the range of 3.6%～5.4%. It indicates that the method is rapid, sensitive and accurate. It was suitable for the determination of the contents of 5 trace heavy metal elements in Fructus Aurantii. The dissolution characteristics of the 5 heavy metal elements in different extraction methods (microwave-assisted extraction, ultrasonic extraction and decocting extraction, respectively) were studied. The results showed that the concentrations of trace elements As and Pb obtained by microwave-assisted extraction were relatively lower than that by ultrasonic extraction and decocting extraction. The dissolving concentrations of the 5 trace heavy metal elements (Cu, As, Hg, Cd and Pb) in Fructus Aurantii in different extracting methods were all lower than the limits of Chinese Pharmacopoeia and Green Trade Standard for Importing and Exporting Medicinal Plant and Preparation. Microwave-assisted extraction for effective constituent was rapid, effective and safe.