The community structure of phytoplankton is one of the important indicators to evaluate the marine ecological environment. At present, the research of this field is mainly based on the on-site sampling followed by laboratory analysis, lacking of rapid on-line automatic, in-situ profile and remote sensing ground verification technology. In order to meet the needs of rapid acquisition of phytoplankton community structure and ground verification of remote sensing data, a fast field measurement method of marine algae community structure based on discrete three-dimensional fluorescence spectrum was studied. Then an in-situ online measurement instrument of marine algae community structure was developed, and at last application demonstration and comparative verification were carried out. The results show that the measurement technology of marine algal community structure based on the discrete three-dimensional fluorescence spectrometry can obtain the algal community structure and chlorophyll content quickly and accurately. Compared with the existing technology, it has the advantages of fast, accurate, stable and reliable measurement, and provides advanced technical means for the acquisition of marine ecological environment monitoring data and ground verification of remote sensing data.