Algal blooms have become a worldwide issue recently, especially those comprised of toxic cyanobacteria. Grazers' predation of bloom-forming algae plays an important role in water clearing. In this study, a species of golden alga (strain ZX1), capable of feeding on the toxic cyanobacteria Microcystis aeruginosa, was isolated and identified as Poterioochromonas sp. (GenBank accession: EU586184) on the basis of morphological characteristics and 18s rRNA gene sequencing. Feeding experiments showed that ZX1 could clear high densities of M. aeruginosa (7.3 × 105–4.3 × 106 cells mL−1) in a short time (40 h), with inhibition ratios higher than 99.9%. ZX1 grew during the feeding processes and achieved a maximum density of 10–20% of the initial M. aeruginosa density. Furthermore, this study is the first to report that ZX1 was able to degrade microcystin-LR (MC-LR) in cells of M. aeruginosa while digesting the whole cells, and that the degradation process was determined to be carried out inside the ZX1 cell. For a total MC-LR (intra- and extracellular) concentration of up to 114 μg L−1, 82.7% was removed in 40 h. This study sheds light on the importance of golden alga in aquatic microbial ecosystems and in the natural transportation/transformation of MC-LR.