Guano are an important factor affecting the cleanliness of photovoltaic modules on floating solar power plants at sea. It can lead to a decrease in photoelectric conversion efficiency, power loss, and even the occurrence of “hot spots”, thereby causing damage to the components. Therefore, the segmentation and detection of guano are crucial for visual automation in the cleaning and inspection processes. However, the composition, density, and thickness of guano naturally vary, leading to inconsistent levels of transparency and color. The uneven intensity of guano images greatly reduces the accuracy of segmentation and detection. Addressing this issue, this study proposes a segmentation algorithm based on combining different color channels to segment guano on the surface of photovoltaic modules. The mean shift method is used for adaptive segmentation to facilitate the detection of guano. Furthermore, the segmentation results obtained by this method are introduced into the input space to improve the traditional Mask RCNN. In addition, this study successfully produced a dataset of guano on the surface of photovoltaic modules using on-site data collection and with the help of a platform built in-house in the laboratory. The experimental results on the self-constructed dataset demonstrate that the enhanced Mask R-CNN model has shown an approximate increase of 5.9% and 6.0% in mAP values for object recognition and segmentation compared to the traditional Mask R-CNN model. This indicates the effectiveness of the methodology proposed in this study.