The invention relates to a measuring method of micro-capsule alga toxin in water. The method includes the steps as follows: firstly, compounding and appraising of the micro-capsule alga toxin; secondly, preparing and purifying of polyclonal antibody antibody: immunizing the New-Zealand rabbit by making the micro-capsule alga toxin holoantigen MC-LR-KLH as the immunity resource, and preparing the polyclonal antibody and purifying by ammonium sulphate according to the normal method; thirdly, preparing immune bead: coupling the micro-capsule alga toxin holoantigen MC-LR-BSA and the nanometer bead, and preparing the immune bead containing MC-LR-BSA; fourthly, embedding the antibody to the pyroxylin film; fifthly, producing testing board, combing the coupling mat of the magnetic scale MC-LR-BSA, the pyroxylin film embedding the polyclonal antibody, the sample mat, the sopping mat, the covering film, the testing board out card into a testing board; sixthly, sample testing, respectively adding standard goods and testing samples with different concentrations into the sampling holds on the testing board, the samples flow on the test paper through the chromatography effect, after 3 to 5 minutes of the reaction under the room temperature, the testing board is put into a magnetic single testing apparatus to be tested, and the testing apparatus can further output the biology reaction signals being transferred to the magnetic field signals by the way of the electric signals; after the standard curve being drawn, the specific value of the micro-capsule alga toxin content in the sample to be tested is counted based on the standard curve.