Underwater vision-based detection plays an increasingly important role in underwater security, ocean exploration and other fields. Due to the absorption and scattering effects of water on light, as well as the movement of the carrier, underwater images generally have problems such as noise pollution, color cast and motion blur, which seriously affect the performance of underwater vision-based detection. To address these problems, this study proposes an end-to-end marine organism detection framework that can jointly optimize the image enhancement and object detection. The framework uses a two-stage detection network with dynamic intersection over union (IoU) threshold as the backbone and adds an underwater image enhancement module (UIEM) composed of denoising, color correction and deblurring sub-modules to greatly improve the framework’s ability to deal with severely degraded underwater images. Meanwhile, a self-built dataset is introduced to pre-train the UIEM, so that the training of the entire framework can be performed end-to-end. The experimental results show that compared with the existing end-to-end models applied to marine organism detection, the detection precision of the proposed framework can improve by at least 6%, and the detection speed has not been significantly reduced, so that it can complete the high-precision real-time detection of marine organisms.