It is a promising way to control Microcystis bloom by the algicidal substances from some special heterotrophic bacteria. However, the algicidal mechanism of the common known 1-hydroxyphenazine and the potential impact of extracellular degradative enzymes from total accompanying heterotrophic bacteria on its algicidal characteristics remains unknown. Here, the physiological changes of Microcystis aeruginosa were investigated under the stress of 1-hydroxyphenazine and extracellular degradative enzymes individually or together. The results showed that the extracellular degradative enzymes from heterotrophic bacteria had a weak inhibitory effect on the growth of M. aeruginosa and made M. aeruginosa suffered oxidative damage. 1-hydroxyphenazine promoted the cells death of M. aeruginosa with a manner independent of reactive oxygen species (ROS) level. 1-hydroxyphenazine might play a role in promoting the cyclic electron transport to reduce ROS in M. aeruginosa. The reduction of total anti-oxidative capacity and the depletion of glutathione might induce the death of M. aeruginosa under stress of 1-hydroxyphenazine. The addition of extracellular degradative enzymes eventually delayed the algae death and alleviated the inhibitory effect of 1-hydroxyphenazine on algal ATPase hydrolytic activity and total antioxidant capacity. The heterotrophic partnership seemed to be helpful to increase the stress resistance of M. aeruginosa.