The cyanobacterium Microcystis aeruginosa can potentially proliferate in a wide range of freshwater bionetworks and create extensive secondary metabolites which are harmful to human and animal health. The M. aeruginosa release toxic microcystins that can create a wide range of health-related issues to aquatic animals and humans. It is essential to eliminate them from the ecosystem with convenient method. It has been reported that engineered metal nanoparticles are potentially toxic to pathogenic organisms. In the present study, we examined the growth inhibition effect of green synthesized copper oxide nanoparticles against M. aeruginosa. The green synthesized copper oxide nanoparticles exhibit an excitation of surface plasmon resonance (SPR) at 270 nm confirmed using UV-visible spectrophotometer. The dynamic light scattering (DLS) analysis revealed that synthesized nanoparticles are colloidal in nature and having a particle size of 551 nm with high stability at -26.6 mV. The scanning electron microscopy (SEM) analysis shows that copper oxide nanoparticles are spherical, rod and irregular in shape, and consistently distributed throughout the solution. The elemental copper and oxide peak were confirmed using energy dispersive x-ray analysis (EDAX). Fourier-transform infrared (FT-IR) spectroscopy indicates the presence of functional groups which is mandatory for the reduction of copper ions. Besides, green synthesized copper oxide nanoparticles shows growth inhibition against M. aeruginosa. The inhibition efficiency was 31.8 % at lower concentration and 89.7 % at higher concentration of copper oxide nanoparticles, respectively. The chlorophyll (a and b) and carotenoid content of M. aeruginosa declined in dose-dependent manner with respect to induction of copper oxide nanoparticles. Furthermore, we analyzed the mechanism behind the cytotoxicity of M. aeruginosa induced by copper oxide nanoparticles through evaluating membrane integrity, reactive oxygen species (ROS), and mitochondrial membrane potential (Δψm) level. The results expose that there is a loss in membrane integrity with ROS formation that leads to alteration in the Δψm, which ends up with severe mitochondrial injury in copper oxide nanoparticles treated cells. Hence, green way synthesized copper oxide nanoparticles may be a useful selective biological agent for the control of M. aeruginosa.