The effectiveness of rehabilitation training methods after ligament injury has become an important factor restricting the future development of athletes. Therefore, the study of sports injuries and rehabilitation training methods for athletes in the new era still has important practical significance. This article mainly studies the effect of nano-ligament combined with sports rehabilitation training on the treatment effect of patients with ligament injury. In this paper, the experimental group received 10–15 minutes of rehabilitation training before each training, while the control group did not. Before and after the experiment, perform functional movement test (FMS) and Y-type balance test (YBT) to compare the differences between the physical functions of the two groups of athletes and the lower extremity exercise ability to test the effectiveness of the rehabilitation training method and help the athletes to recover quickly after injury restore. The score comparison between the two groups on the first day of treatment was p > 0.05, and there was no statistically significant difference between the two groups; the score comparison between the third day of treatment and four weeks after treatment was p < 0.05, and the difference between the two groups was statistically significant, A the curative effect of the group was better than that of group B; the score comparison at eight weeks after treatment was p > 0.05, and there was no statistically significant difference between the two groups. There was no significant difference between the FMS test results and the YBT test results of the experimental group before the experiment. The test results of the experimental group after the experiment were significantly higher than the control group (significant difference), indicating that rehabilitation training helps improve and improve physical exercise ability, especially for improvement. The athlete’s lower extremity athletic ability has obvious effect.