A novel nonenzymatic immunosensor for sensitive detection of Microcystin-LR (MC-LR) is constructed using a graphene platform combined with mesoporous PtRu alloy as a label for signal amplification. Primary antibody-Microcystin-LR (Ab1) is immobilized onto the surface of a graphene sheet (GS) through an amidation reaction between the carboxylic acid groups attached to the GS and the available amine groups of Ab1. Mesoporous PtRu alloy, prepared by corrosion PtRuAl alloys, is employed as a label to immobilize secondary antibody (Ab2). The resulting nanoparticles, PtRu-Ab2, are used as labels for the immunosensor to detect MC-LR. Under optimal conditions, the immunosensor exhibits a wide linear response to MC-LR that ranges from 0.01 to 28 ng·mL−1, with a low detection limit of 9.63 pg·mL−1 MC-LR. The proposed immunsensor shows good reproducibility, selectivity, and stability. The assayed results of polluted water with the sandwich-type sensor are acceptable. Importantly, this methodology may provide a promising ultrasensitive assay strategy for other environmental pollutants.