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Geosmin (GSM) and 2-methyl isoboneol(2-MIB) are the major compounds causing the odor of water body. A new method for the qualitative and quantitative analysis of GSM and 2-MIB, which isolated and enriched the odor compounds from the water samples by using Headspace solid-phase micro extraction (HS-SPME), and detected the two substances using GC/MS with internal standard method, was developed. The optimal conditions of HS-SPME for GSM and 2-MIB were as follow: extracting for 40minute, extracting at 65°C, and adding NaCl 0.1g. The temperature program for column of GC was first maintained at 50 °C for 1 minute, then rose to 100 °C at the rate of 10°C per minute keeping for 0.15minute, finally rose to 240°C by 5°C per minute. Under these conditions, the separate detection limits of GSM and 2-MIB were obtained with 0.2ng / L and 0.5ng / L. The relative standard deviations were 5.37% and 5.56% respectively. This method applied for measuring the actual water samples of Longtan Lake and Taihu Lake in December. The former contained 1.26ng/L of GSM and 1.074ng/L of 2-MIB, while the latter included 2.681ng/L of GSM and 3.392ng/L of 2-MIB.