The study of algae is significant for monitoring marine environment and exploring biological resources. Confocal Raman spectroscopy has been widely used in biology as a label-free and rapid detection technique. Currently, the commercial micro-Raman is dominated in this field, while it is not applicable to field measurements for the instrumental size and the operation condition. Hence, a fiber optic spectrometer is introduced to develop a low-cost compact confocal-raman system for algae detection at “single-cell” level. The developed system is all-in-one designed for the compactness, and is well functioned with the capacities of Raman detection, microscopic imaging and optical tweezers capture. Four typical kinds of single-cells (Skeletonema costatum, N.oceanica IMET-1, Prorocentrum donghaiense Lu and Chlorella) were used to evaluate the system detectability, and the components such as proteins, lipids, glycogen and nucleic acids were recognized. Based on that, the algae cells were successfully classified into 4 species after using principal component analysis (PCA) method, which indicates that it is feasible to apply the fiber optic spectrometer for single cell analysis of marine microbes. It is expected that the developed system will be deployed as field instrument for the deck measurements in sea trials in the future.