The invention relates to a multifunctional epiphytic algae collecting instrument which comprises a collecting cylinder, an automatic rotating brush, a liquid extractor and an air pump, wherein the collecting cylinder comprises an outer ring wall, an inner ring wall, an air suction pipe, an outer wall suction cup, an inner wall suction cup and a fixing plug; the automatic rotating brush is freely inserted inside the collecting cylinder, and comprises a rotating column, an electric handle mounted at an upper end of the rotating column, a starting button mounted on the electric handle, and a steel brush mounted at a lower end of the rotating column in a matching manner. The multifunctional epiphytic algae collecting instrument provided by the invention is simple and reasonable in structural design, convenient to disassemble, portable, high in safety during qualitative and quantitative sampling, high in precision, small in error, sturdy, durable, simple in operation, and suitable for collecting epiphytic algae in various water area environments.