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Grass carp hemorrhagic disease (GCHD), which is induced by grass carp reovirus (GCRV), stands as one of the most severe communicable diseases jeopardizing freshwater aquaculture, creating a demand for innovative, effective, and affordable surveillance tools. Machine vision can serve as a powerful inspection method, enabling early alerts for GCHD epidemic spread. Yet, experimental dataset tests indicate that the detection precision of existing deep learning algorithms remains unsatisfactory. In the present study, image datasets of the model organism Chinese rare minnow (Gobiocypris rarus) manifesting GCHD signs were gathered, and a self-attention-based convolutional neural network (SA-CNN) deep learning architecture was designed. This SA-CNN framework is capable of reliably pinpointing Chinese rare minnow individuals displaying GCHD symptoms. Through pre-processing the extracted imagery using refined k-means and improved watershed algorithms, tightly clustered or superimposed fish can be adaptively disentangled within populations, thereby elevating recognition accuracy. With an optimized loss function, the SA-CNN model delivers an accuracy of 99.1%, a recall of 97.7%, and an F1 score of 96.6% on the collected datasets of symptomatic fish. Its precision outperforms current state-of-the-art you only look once (YOLO) network families by margins between 4.9% and 25.6%, varying across different model variants. Image identification demands a mere 95ms per frame, highlighting considerable operational efficiency. Ablation studies confirmed that incorporating the self-attention module yielded accuracy gains of 3.8% and recall improvements of 3.0%. Accordingly, this refined SA-CNN framework furnishes an efficacious solution for the essential large-scale deployment of GCHD surveillance initiatives tracking GCRV transmission, paving the way toward intelligent, health-oriented, and precision aquaculture.