Ship ballast water can control the roll, trim, and draft of the ship, and thus ensuring the balance and stability of the ship in the course of sailing, and playing a vital role in the safe navigation of ships. The annual discharge of ship ballast water is very large in China. About three to five billion cubic meters of ship ballast water is discharged into offshore or inland waters every year. This water contains plankton, pathogens, and their larvae or spores. If not be handled appropriately, this will have a serious impact on the ecological environment of the discharge waters. Ballast water is usually treated by electrolysis before being discharged. Sodium hypochlorite can be generated, which can kill microorganisms; however, the by-products trihalomethanes (THMs) are cytotoxic and biotoxic. Studies have shown that THMs may cause fetal growth retardation, spontaneous abortion, or death. The concentration of THMs in drinking water is closely related to the risk of bladder cancer death. Hence, it is important to establish a method for the determination of THMs in ship ballast water. The four kinds of THMs are chloroform, dichlorobromomethane, chlorodibromomethane, and tribromomethane. At present, ship ballast water is mostly analyzed by gas chromatography (GC) using an electron capture detector (ECD) or by gas chromatography-mass spectrometry (GC-MS). Given the low boiling point of THMs, headspace injection and purge-and-trap can be used. Gas chromatography-negative chemical ionization-mass spectrometry (GC-NCI-MS), was adopted. NCI is a soft ionization technique that shows special response to compounds bearing electronegative elements or groups. THMs contain electronegative chlorine atoms and bromine atoms. Therefore, NCI is a good choice for their analysis. The samples were processed by the headspace injection technique. The NaCl content in 10 mL sample was optimized in headspace injection. The results showed that 3.0 g NaCl was the most suitable dosage. The analytes were separated on a DB-5MS UI capillary-column (30 m×0.25 mm×1.0 μm). The target compounds were quantified by using the external standard method in selected ion monitoring (SIM) mode. The four THMs were not only well separated but also showed a high response at 0.2 μg/L. The four THMs showed good linear relationships in the range of 0.2-50 μg/L, with correlation coefficients≥0.995. The limits of quantification (LOQs, S/N =10) were 0.1-0.2 μg/L, and the average recoveries of the four THMs were 90.3%-106.8% at the three spike levels of 0.2, 0.5, and 2.0 μg/L. The relative standard deviations were 1.4%-6.2%. The LOQs of the THMs in the GB/T 5750.8-2006 Standard Test Method of Drinking Water Organic Matter Index are 0.3-6.0 μg/L. It can be seen that the LOQs of the THMs are greatly reduced in this study. The proposed method is accurate, stable, and reliable, and it can be used for monitoring the four THMs in ship ballast water. The method was applied for the detection of 36 ship ballast water samples. In all cases, the detection rates of tribromomethane, chlorodibromomethane, dichlorobromomethane, and chloroform were 83.3%, 69.4%, 22.2%, and 19.4%, respectively. The detection values of tribromomethane, chlorodibromomethane, dichlorobromomethane, and chloroform were 34.25-221.5 μg/L, 3.52-41.87 μg/L, 1.52-8.56 μg/L, and 0.02-5.46 μg/L, respectively. Based on the analysis of several ship ballast water samples (electrolytic water), it was concluded that the greater the number of bromine atoms in the THMs, the higher are the detection rate and detection value in ship ballast water. Compared to chloroform, tribromomethane is more harmful to living beings. China has acceded to the International Convention on Ship Ballast Water and Sediment Control and Management. There is an urgent need to establish analysis methods with high sensitivity, good stability, and high accuracy in addition to determining standards and regulations for ship ballast water.