The invention discloses a method used for screening and identifying saxitoxins in complex matrix. The method comprises following steps: 1, preparation of a matrix sample; 2, matrix sample purification, and toxin separation; 3, establishment of a mass spectrometry database; 4, sample information acquisition and result determination; 5, high resolution mass spectrum measuring of suspected positive samples and metabolic products of the suspected positive samples; and 6, qualitative measurement used for determining accurate molecule mass. According to the method, the mass spectrometry databases of 24 kinds of saxitoxins are established, the method can be used for high precision qualitative analysis in sample screening processing, realizing blind measuring of toxic-free standard samples and accurate qualitative determination, solving problems in the prior art that standard substances are expensive, arrival period is long, and the standard substances are controlled by entry and exit administration, and reducing detection cost in daily monitoring; requirement on the technical level of operation staff in saxitoxin detection is reduced; and operation is convenient.