Objective To design a device for studying the effects of shear stress on the activity of blue-green algae. Methods The device was optimized in terms of the weakness of current shear stress devices, such as small volume, unstability, inability for quantitative analysis and short working period. The effective volume of the new device was 400-700 mL, and the error was less than 13.8%. Moreover, this device could produce a quantitative and uniform shear stress field and be continued to follow observation for more than 96 hours. Results By experiment on growth of microcystis aeruginosa, the device was proved to generate shear stress that could significantly affect the activity of microcystis aeruginosa cells. Conclusions This experimental device is an effective equipment for investigating the effects of shear stress on the activity of blue-green algae.