The invention belongs to the technical field of biological analysis and detection, in particular to a microfludic chip for rapid detection of microcystins and a preparation method thereof. The microfludic chip is made of optically transparent polydimethylsiloxane and the like by a molding method, and mainly comprises a sample reaction microchannel layer, a valve control layer and a substrate layer. The microfludic chip comprises a sample enriched and immunoassay module which consists of parallel immune chromatographic column microanalysis chambers in nanolitre volume. Microcystin antibody proteins or antigens are fixed in each analysis chamber, and rapid on-site detection of representative algal toxins, namely microcystins in samples with different sources is realized. Besides the advantages of high sensitivity and specificity, the microfludic chip has the characteristics of rapidness, high efficiency, portability, low cost and easily automatic control, can finish automatic signal acquisition, remote transmission and signal analysis, and is suitable for on-site rapid detection and remote control detection in a wide range for the microcystins in the water environment.