The invention relates to a method for screening single chain antibodies of Microcystin-LR and verification thereof. The method comprises the following steps: carrying out two rounds of affinity screening on the biotinylated Microcystin-LR in a human source synthetic antibody library by using an avidin labeled magnetic bead and a negative screening method; extracting total plasmid DNA from phage colonies produced in the second round, carrying out enzyme digestion with enzyme Sfi I, recycling gel to obtain single chain antibody genes, connecting the single chain antibody genes with soluble expression carrier pAK100CL which is processed by enzyme digestion in the same way, and electrically transforming the connected carrier into colibacillus XL1-Blue to obtain soluble expression single chain antibodies; and verifying the soluble expression single chain antibodies by using a competitive time-resolved fluorescence immune analytical method. The invention has the advantage of quick, simple and convenient screening, and can well expose the Microcystin-LR three-dimensional structure into the incubation system. The verification on the screening result has the advantages of high detection signal and strong anti-interference capacity against stroma.