The invention discloses a method used for measuring the viscosity coefficient of cyanophyta microcystis. The method comprises following steps: 1, water samples containing cyanophyta microcystis are collected, the initial total concentration C0 and the initial total integration rate phi of unicell and and cell colonies are obtained; 2, the water sample are delivered into the internal external barrel gap of an external barrel rotating type Couette device, the external barrel rotating speed is adjusted until the generated laminar shear rate G is constant and ranges from 5s<-1> to 50<-1>, wherein the relation of G with the rotating speed is displayed by a formula in the invention, N is used for representing external barrel rotating speed, R is used for representing internal barrel semidiameter, R2 is used for representing external barrel semidiameter, and rotating time ranges from 20 to 60min; and 3, after rotating, the initial total concentration Ct of unicell and and cell colonies is obtained; and 4, the viscosity coefficient alpha of cyanophyta microcystis is calculated based on a formula in the invention, wherein t is used for representing rotating speed. Operation of the method is simple and convenient; equipment cost is low; the viscosity coefficient is obtained via the method; and technical means are provided for study on cyanobacterial bloom burst.