Previous studies showed that the petroleum ether extracts from the submerged macrophytes Potamogeton crispus significantly inhibited the growth of Karenia mikimitoi. Further, four antialgal activity compounds (1-4) were successfully isolated through a combination of silica gel column chromatography and repeated preparative thin-layer chromatography in this paper. These four antialgal compounds showed antialgal activities against K. mikimitoi. Furthermore, their structures were identified on the basis of spectrum data. There are pentacosyl alcohol, 1, 2-benzenedicarboxylic acid, 1, 2-bis(2-methylhexyl) ester, palmitic acid, and 1, 2-benzenedicarboxylic acid, 1, 2-bis(5,5-methylhexyl) ester. These four compounds were isolated from P. crispus for the first time, and compounds 1, 2, and 4 were isolated from the submerged macrophytes for the first time. This paper provided solid experiment foundation for further study. Furthermore, at the concentration of 50 μg/mL, these four antialgal compounds significantly inhibited the growth of Heterosigma akashiwo; and pentacosyl alcohol and 1, 2-benzenedicarboxylic acid, 1, 2-bis(5,5-methylhexyl) ester exhibited more significant antialgal activity against Prorocentrum donghaiense and Phaeocystis globsa.