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Long-term, automated fish detection provides invaluable data for deep-sea aquaculture, which is crucial for safe and efficient seawater aquafarming. In this paper, we used an infrared camera installed on a deep-sea truss-structure net cage to collect fish images, which were subsequently labeled to establish a fish dataset. Comparison experiments with our dataset based on Faster R-CNN as the basic objection detection framework were conducted to explore how different backbone networks and network improvement modules influenced fish detection performances. Furthermore, we also experimented with the effects of different learning rates, feature extraction layers, and data augmentation strategies. Our results showed that Faster R-CNN with the EfficientNetB0 backbone and FPN module was the most competitive fish detection network for our dataset, since it took a significantly shorter detection time while maintaining a high AP50 value of 0.85, compared to the best AP50 value of 0.86 being achieved by the combination of VGG16 with all improvement modules plus data augmentation. Overall, this work has verified the effectiveness of deep learning-based object detection methods and provided insights into subsequent network improvements.