The intelligent algae density analysis system utilizes machine vision, deep learning, and automated control technologies, combined with high-performance computing and big data technologies, to simulate human vision and the brain. Through electron microscope imaging, it distinguishes the shape, texture, color, flagella, light transmittance, and cell nodes of algae, enabling rapid and accurate identification of various algae species in water samples and efficient calculation of algae density. This system is applicable to environmental monitoring stations, waterworks, and water quality environmental protection centers where water quality and algae analysis and monitoring are required. It can identify more than 50 species of algae, including Cyanophyta, Chlorophyta, Bacillariophyceae, and Dinophyta.