Harmful cyanobacterial blooms (HCBs) threaten aquatic ecosystems globally, but eco-friendly biological controls are limited by insufficient engineering applications and unclear ecological feedback. In this study, we isolated Bacillus sp. HH1 (HH1) from Lake Tai's HCBs-polluted areas and evaluated its cyanobactericidal efficacy and ecological impacts via laboratory assays, simulated ecosystems (light/moderate/severe HCBs), and field applications. Results showed that HH1 exhibits highly-efficiency cyanobactericidal activity across diverse water bodies in a dose-dependent way and 1.1 × 10⁵ CFU/ml HHI could reach 92 % of cyanobactericidal rate within 4 days. HH1 induced algal death via oxidative damage, structural disruption, and photosynthetic interference but increased bacterial community diversity and stability and promoted deterministic processes (increasing their contribution to community assembly to 86.67 %). The continuous proliferation of bacteria promotes the enrichment of pollutant-degrading functional microbiota, ultimately promoting the ammonia nitrogen, total nitrogen, total phosphorus, and chemical oxygen demand removal in water column. Notably, HH1 remediated water through a cascade: cyanobacteria elimination → community reconstruction → enhanced pollutant degradation →nutrient reduction, achieving concurrent HCB control and water quality improvement. Critically, HH1 offers a low-cost and scalable choice for HCBs emergency management, aiding developing countries in achieving Sustainable Development Goals 6.