Eutrophication of environmental waters and occurrence of harmful cyanobacterial blooms have drawn much attention all over the world. For controlling cyanobacteria overgrowth, biological control methods such as anticyanobacterial process by microorganisms have been recently explored. In this study, a Streptomyces strain named HJC‐D1 is isolated from an eutrophic pond in China, which exhibited anticyanobacterial activity against a representative bloom‐forming cyanobacterium Microcystis aeruginosa. Based on its morphology and 16S rRNA sequence, the isolated strain is identified as Streptomyces sp. Results show that the M. aeruginosa is biodegraded by the isolated strain HJC‐D1, and the Chl a removal efficiency is 53.5 ± 4.3%–62.6 ± 3.3% at the initial Chl a concentration of 0.2713–0.6375 mg L−1. The anticyanobacterial mechanism of Streptomyces sp. on M. aeruginosa is that the growth of cyanobacterial cell is destroyed by the active substances secreted by strain HJC‐D1, and TEM results demonstrate the degradation processes are divided into three steps: cell breakage, organelle release, and cell death. The isolated microorganism may be a potential environment‐friendly strain and provides a possible approach for Microcystis bloom control in lakes and reservoirs.