For the detection of cyanobacterial toxin, an Enzyme-linked immunosorbent assay (ELISA) was integrated into a PDMS microchip. The conjugates of microcystin-LR (MCLR) and keyhole limpet hemocyanin (KLH) were adsorbed on the surface of polystyrene beads and these MCLR-KLH polystyrene beads were introduced into a microchamber. MCLR on the surface of polystyrene beads reacted with horseradish peroxides (HRP) conjugated anti-MCLR monoclonal antibody (mAb) which had a competitive reaction with MCLR in water sample. After the enzyme substrate 3,3,5,5-tetramethyl benzidine (TMB) was injected into the chamber and catalyzed by HRP, the color change was detected with a liquid-cord waveguide. This integration shortened the conventional ELISA analysis time from several hours to about 30 min with only 4.2 $mu$L MCLR sample consuming which was useful for the environmental analysis. More over, troublesome operations required for ELISA could be replaced by simple operations. The microchip based detection system showed a good sensitivity of 0.05 $mu$g/L and maintained good reliability through its quantitative range with low coefficients of variation (2.5-10.5%).