Currently, aquaculture methods tend to combine scale and intelligence, which saves manpower and improves the survival rate of seafood at the same time. High-precision and high-efficiency fish individual recognition can provide key technical support for fish disease detection, feeding habits, body condition, etc. In the realm of intelligent aquaculture, it provides robust data support for precision fish farming. However, the current research methods for individual fish recognition struggle to maintain the network model's focus on the fish body in real marine underwater complex environments (e.g., environmental background interference such as coral reefs, overlap between fish bodies, light noise, etc.), leading to unsatisfactory recognition results. To this end, this paper proposes a method for fish individual recognition in underwater complex environments based on video object segmentation, which consists of three parts, including a fish individual segmentation detection module, a fish individual recognition module, and an all-in-one visualization module. The work adopts a combination of deep learning methods and video object segmentation algorithms to solve the problem of low attention and poor detection accuracy of fish individuals in real underwater complex environments, which effectively improves the accuracy and efficiency of fish individual recognition, and analyzes and discusses the comparison of recognition effects using different weights. The results of the simulation experiments show that the key metric Rank1 value of the method achieves more than 96% accuracy on the public datasets DlouFish, WideFish, and the Fish-seg dataset produced in this paper, and improves over the state-of-the-art methods for fish individual recognition by 2.23%, 1.33%, and 1.25%, respectively.