Background: Corneal fluorescein staining is a key biomarker in evaluating dry eye disease. However, subjective scales of corneal fluorescein staining are lacking in consistency and increase the difficulties of an accurate diagnosis for clinicians. This study aimed to propose an automatic machine learning-based method for corneal fluorescein staining evaluation by utilizing prior information about the spatial connection and distribution of the staining region. Methods: We proposed an end-to-end automatic machine learning-based classification model that consists of staining region identification, feature signature construction, and machine learning-based classification, which fully scrutinizes the multiscale topological features together with conventional texture and morphological features. The proposed model was evaluated using retrospective data from Beijing Tongren Hospital. Two masked ophthalmologists scored images independently using the Sjogren's International Collaborative Clinical Alliance Ocular Staining Score scale. Results: A total of 382 images were enrolled in the study. A signature with six topological features, two textural features, and two morphological features was constructed after feature extraction and selection. Support vector machines showed the best classification performance (accuracy: 82.67%, area under the curve: 96.59%) with the designed signature. Meanwhile, topological features contributed more to the classification, compared with other features. According to the distribution and correlation with features and scores, topological features performed better than others. Conclusions: An automatic machine learning-based method was advanced for corneal fluorescein staining evaluation. The topological features in presenting the spatial connectivity and distribution of staining regions are essential for an efficient corneal fluorescein staining evaluation. This result implies the clinical application of topological features in dry-eye diagnosis and therapeutic effect evaluation.