At present, the extraction of the soluble organic matter is mainly applied to sedimentary rocks for exploring oil and gas. The contents of the soluble organic matter in UHP metamorphic rocks from CCSD are usually at the level of trace amounts. It is therefore very important to prevent pollution from drilling mud, sample preparation and processing analysis and to improve extraction efficiency. This paper has dealt with the removal of external contaminants, the improvement of the extraction efficiency by ultrasonic wash, Soxhlet extraction and ultrasonic extraction, and the elimination of pollution in core samples by comparing total ion chromatogram between the samples and the pollutants.