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Background: Qiangji Jianli Fang (QJF) has been used for treatment of myasthenia gravis (MG) in China. However, our understanding of the effects of QJF against MG at the molecular level is limited. This study aims to investigate the effects of QJF treatment of MG patients on the protein, peptide and metabolite levels in serum., Methods: High-throughput proteomic, peptidomic and metabolomic techniques were applied to investigate serum samples from 21 healthy individuals and 47 MG patients before and after QJF treatment via two-dimensional gel electrophoresis, matrix-assisted laser desorption/ionization time of flight mass spectrometry and liquid chromatography Fourier transform mass spectrometry, respectively., Results: After QJF treatment, the expression levels of peptides m/z 1865.019, 2021.128 and 1211.668 of complement C3f increased (P = 0.004, P = 0.001 and P = 0.043, respectively), while that of peptide m/z 1739.931 of component C4b decreased (P = 0.043), in the serum of MG patients. The levels of γ-aminobutyric acid (P = 0.000) and coenzyme Q4 (P = 0.000) resumed their normal states., Conclusion: QJF could inhibit the activity of the complement system and restore the normal levels of metabolites.