Abstract: Electrospray ionization time-of-flight mass spectrometry (ESI-TOF MS) is one of the important tools for structure identification of molecules in drug research and development, in particular, the accuracy mass measured by high-resolution mass spectrometer can provide the information regard to elemental composition for the test compound. In recent years, with the rapid development of pharmaceutical industry, the demand for high-resolution mass spectrometer is increasing in the field of pharmaceutical research and development. The self-developed high-resolution time-of-flight mass spectrometer API-TOF MS 10000 has been designed in Guangzhou on 2011. The mass resolution of 10 000 can be achieved and the instrument detection limit is less than 2.5 μg/L (reserpine), mass ranges cover 30-5 000 Da. In order to verify the performance of this equipment for structure identification and the determining accurate mass of drug molecules, 291 natural products and synthesis products were analyzed on API-TOF MS 10000. Sodium trifluoroacetate was used as internal standard substance to calibrate the instrument, and the relative mass error was obtained by comparing the measured and theoretical mass. The molecular weights of 248 compounds determined by the machine are accord with their identified results, which have a large range of molecular weight from 145 to 5 826 Da. And the 248 compounds cover most of the chemical structure of natural products, such as flavonoids, alkaloids, lignins, phenylpropanoids, coumarins and so on. Accurate mass measurements were performed to confirm 202 compounds’ formula. The results reveal that all the relative mass error is less than 5×10^-6, 76.7% of the relative mass error is less than 2.5×10^-6. Other results (43 compounds) were inconsistent with the expected structure indicating the original proposed structure was wrong and the other spectra were also provided information to demonstrate the point. In conclusion, the domestic time-of-flight mass spectrometer can accurately determine the mass of drug molecules and isotope abundance ratio, and it has been demonstrated as a powerful tool to provide the molecule and formula information for structure elucidation of pharmaceutical molecules.