It is still difficult to directly detect low content of volatile organic compounds (VOCs) in water samples by gas chromatography (GC) because when water is the only solvent, it would result in the instability and poor repeatability of peak retention time and peak shape. The adverse effects of water on direct GC analysis of VOCs cannot be significantly reduced or eliminated by simply changing the detection condition of GC. However, it was found that the addition of methanol in samples to a certain final proportion, such as 50 or 75% (v/v), could greatly reduce or eliminate the adverse effects of water. By using 75% (v/v) methanol as a solvent, the standard curves of ethanol, acetic acid, acetone, and isopropanol with correlation coefficient (R 2) over 0.99 were successfully plotted by gas chromatography-flame ionization detection (GC-FID) in a certain concentration range, respectively. The results showed that the retention time and peak shape stability of ethanol, acetic acid, acetone, and isopropanol in aqueous solution were greatly improved by the addition of methanol to final concertation of 75% (v/v). To verify the practical application potential of this method, the method was applied to the detection of components in isopropanol fermentation wastewater. The results showed that the method has well applicability and reliability. The key points in the application of this method were also summarized. This GC analysis method would have a wider and better application prospect in the detection of water-soluble organic matters.