Objective To establish a qualitative and quantitative method to determine ammonia in biological samples by gas chromatography-mass spectrometry （GC-MS）. Methods A heptafluorobutyryl chloride derivatization method was used. GC-MS was used for determination. The effects of different pH conditions, derivatization temperature, time and different extraction solvents on the test results were investigated. The pretreatment conditions were optimized. Results This method could accurately detect the ammonia content in blood, and the limit of detection was determined to be 0.1 μg/mL. The target component showed good linearity in the range of 0.5-200.0 μg/mL （R2=0.987 7）. The relative standard deviation range of intra-day precision was 2.59%-3.88%. The relative standard deviation range of inter-day precision was 3.21%-3.76%. Conclusion The method showed good sensitivity, stability and specificity, therefore can be used for forensic toxicology analysis and clinical biochemical detection.