A method combining solid phase microextraction (SPME) with cryofocus technique was developed for the compound-specific carbon isotope analysis of volatile organic compounds in aqueous phase. The detection limit was 10 times better than the conventional SPME method. Under the optimized analytical conditions, aqueous samples of trichloroethylene/perchloroethylene (TCE/PCE) (20 microg/L) and benzene/toluene (10 microg/L) were analyzed. The delta 13C fractionation compared to pure-phase and headspace analysis was less than 0.5 per thousand. The standard deviation was 0.3 per thousand. The method was applied to the delta 13C analysis of PCE in a contaminated groundwater in Beijing. The delta 13C values of PCE on site B408 (source area) and site B230 (spilled area) were -37.8 per thousand and -34.45 per thousand, respectively. The enriched delta 13C value on site B230 may be caused by biodegradation or chemical reaction in groundwater. The tested delta 13C value of benzene, toluene, trichloroethylene and perchloroethylene from different manufacturers were different, indicating that carbon isotope analysis is a useful method to distinguish the sources of contaminants in the environment. This method is simple, easy to use and highly sensitive. It is suitable for the compound-specific carbon isotope analysis of volatile organic compounds in aqueous phase.