Abstract: High resolution mass spectrometry is a powerful tool for non-target screening of a wide range of compounds, and the accurate mass measured by high resolution mass spectrometry could facilitate prediction of molecular formula of the compound, thus laying the foundation for further compound screening. A molecular formula calculator FM-searcher based on molecular formula database strategy was developed to improve top hits ratio of molecular formula prediction with high-resolution mass spectrometric data in non-target screening, and providing more reliable reference information for further screening of a compound. Based on the core idea of “Existence is reasonable, and a large number of existences are stable”, the software could calculate and sort the molecular formula according to the frequency of the molecular formula in the existing compound database, so as to judge the rationality of the molecular formula calculation and the top hits ratio. Based on a total of 219 accurate molecular weights of veterinary drugs, biological toxins and other hazardous substances obtained from the determination and collected from literatures, the top hits ratio of the formula calculated by FM-searcher was compared with that obtained by ordinary algorithm (the calculator in Xcalibur). The results showed that FM-searcher could achieve a higher top hit ratio without any element limitation; the top 5, top 3 and top 1 hit ratio are 91.8%, 82.6% and 50.7%, respectively. While for ordinary algorithm, the top 5, top 3 and top 1 hit ratio are 21.0%, 15.1% and 6.4% in the case of broad elements limitation; and in the case of precise elements limitation according to subcategories, the corresponding data results are 82.2%, 69.9% and 48.9%, respectively. Compared with the conventional method, this method could improve the hits ratio under broader element limitation, simplify the formula prediction process and improve efficiency with simple operation and practicability. The molecular formula of accurate mass measured in the actual sample matrix was also calculated, FM-searcher could still achieve a higher top hits rank of correct formula than an ordinary molecular formula calculator.