Utilization of allelochemicals to inhibit overgrowth of toxic cyanobacteria is considered to be an environmentally friendly approach. However, the regulatory role of the signaling molecule nitric oxide (NO) on cyanobacteria under allelopathic stress remains unanswered. Here we demonstrate that the effect of NO on the cyanobacterium Microcystis aeruginosa depends on allelopathic stress of pyrogallic acid (PA). The experimental results revealed that general stimulation of M. aeruginosa by PA occurred within the concentration range 0.4–0.8 mg/L. In parallel with increasing concentration of PA (1.6–16.0 mg/L), the growth of M. aeruginosa was observed to decrease. The effect of NO on M. aeruginosa was evaluated by addition of the NO scavenger hemoglobin. In the stimulation stage, intracellular NO was seen to decreased to modulate the level of reactive oxygen species (ROS) and to maintain redox homeostasis of the cells. In the inhibition stage, the physiological characteristics of M. aeruginosa were changed significantly. Additionally, the accumulation of S-nitrosothiol by M. aeruginosa indicated that the high concentrations of PA induced nitric oxidative stress in M. aeruginosa. This study provides a new thought to understand the role of NO in controlling harmful algal blooms through the allelopathic effect of aquatic macrophytes.