From November 2021 to November 2022， the algae in the Erhai Lake Basin were compared by instruments and manual detection. By analyzing the comparison data， the accuracy， consistency and application scope of the instruments were discussed and verified. The results show that the cell density and species number of algae detected by the instrument are higher than those detected manually， but the changing trend is generally consistent， which can reflect the change of algae to some extent. The density of algae cells needs to be adjusted for instrument detection. The most suitable density of algae cells is 10~30 million cells/L， the relative deviation of instrument comparison is ± 40%， and the relative deviation of instrument twice counting results is ± 20%， which is suitable for trend research and monitoring with low requirements on data accuracy. The method detection limit of the instrument is 2.4×10⁴ cells/L when the sample is concentrated 5 times， and the detection limit verified by the blank experiment is higher than the method detection limit. For samples containing many impurities or plant debris， instrument detection yields many errors， making manual detection more suitable. When the density of algae cells in samples is lower than 5 million /L or higher than 100 million /L， the instrument detection can be too high or too low， with relatively large errors. In such cases， it is necessary to perform detection after concentration or dilution treatment or conduct manual detection instead.