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Image analysis based on biological morphological differences is an important development direction for classification and determination of planktonic algae. However, it has some shortages, such as high degree of sample imbalance and difficult to have formalized description of local physiological features. To overcome these shortages, this study decomposed recognition of harmful algae microscopic images into sample supplementation, accurate segmentation, feature extraction and classification and identification. Firstly, sample imbalance is solved by Kernel-ADASYN method to generate enough samples. Target cells are separated through integration of multi-directional projections. Refined segmentation between the spine and cingulum detail regions is further realized. Later, effective feature extraction and description of global and local features were performed one by one by matching physiological features of algae with machine recognition features. Finally, the SVM model was applied for multi-class recognition. Results demonstrated that the proposed method can reduce imbalance rate of sample size and realize multi-class recognition of microscopic images of 15 categories of algae cells.