The invention discloses a water quality conditioner for inhibiting harmful algae, which mainly comprises the following components in percentage by weight: 10-60% of soluble silicon metered based on SiO2, 10-60% of calcium oxide, 1-20% of magnesium, and 1-25% of phosphorus. When the water quality conditioner is in use, the components are proportioned and uniformly mixed to form a blending agent, and the blending agent is scattered on a water surface in a dry way in the morning in a selected clear day, with 5-10kg per mu. The water quality conditioner can fully meet the nutrition and ecologicalrequirements of the bloom of beneficial algae such as microalgae so as to ensure that the microalgae beneficial to aquaculture is greatly bloomed and harmful algae such as blue-green algae is inhibited; after the water quality conditioner is applied for 3-7 days, the water body is improved, the beneficial algae such as the microalgae is bloomed while the harmful algae such as the blue-green algaeand the like are massively extincted, and the water body becomes rich, active, delicated and clear. The invention can be widely applied to various water areas such as ponds, reservoirs, lakes, coastal sea and the like and the treatment and prevention of the harmful algae in the culture of fishes, shrimps and crabs, and has no damage to human bodies and aquatic organisms.