Background: Modified Tabusen-2 decoction (MTBD) is Traditional Chinese Mongolia Medicine, it is consist of “Lancitou” “Duzhong” “Sanqi” and “Honghua”. MTBD is mainly used to treat osteoporosis. However, the precise material basis of this prescription is not yet fully elucidated, which affects its modernization developmentMethods: We establish a new HPLC-QE Orbitrap MS technology with four-steps characteristic ion filtering (FSCIF) strategy to quickly and effectively identify the structural features of MTBD, and determine the representative compounds content. Then the quantitative method of nineteen main components in MTBD were built, and eight batches MTBD were determined as well. Results: By using the FSCIF strategy, a total of 143 compounds were unambiguously or tentatively identified, including 5 compounds were first reported in MTBD. Nineteen representative components were simultaneously quantified by HPLC-QE Orbitrap MS, and it is suitable for eight batches of MTBD. Methodology analysis showed that the assay method of 19 compounds (including three pairs of isomers) with a good repeatability, accuracy, and stability. Conclusion: The method established above was successfully applied to assess the quality of MTBD extracts, which prove that the concentrations of 19 compounds varied significantly in different batches of MTBD extracts. Collectively, our findings enhance our molecular understanding of the MTBD formulation and will allow us to control its quality in a better way. At the same time, this study can promote the development and utilization of ethnic medicine.