The invention discloses a method and system for increasing judgment accuracy of monoisotopic peaks. The method comprises the following steps: according to selected tandem mass spectrums, determining candidate isotopic peak clusters; according to the similarity and the strength ratio of the chromatographic outflow curves of the candidate isotopic peak clusters, determining the start and stop of the isotopic peak clusters; according to the start and stop of the isotopic peak clusters, determining the quality of the monoisotopic peaks; and judging whether the monoisotopic peaks of the tandem mass spectrums are not determined or not, if yes, returning and selecting a new tandem mass spectrum to determine a candidate isotopic peak cluster, and if not, ending.