In this paper, 20 basketball players from each of the three universities who participated in the Guangdong University Basketball League, total 60 persons, were used as experimental subjects. Each university was divided into an experimental group of 10 players and a control group of 10 players for a 12-week comparison experiment. The experimental group was trained using CrossFit program and the control group was trained using traditional physical training methods. The six indexes of body shape, strength, speed, endurance, flexibility and agility were taken as the physical fitness evaluation indexes, and the corresponding test items were body fat percentage, standing long jump, bench press, squat, deadliftl, 3/4 full-court sprint run, 15×17 folding run, 3000 meters run, seated body flexion, and T-word agility test, a total of 10 test items. The data collected before and after the 12 weeks of training were statistically and analytically analysed through the use of EXCEL and SPSS26.0 software. To explore the effects of CrossFit training on athletes' physical fitness relative to traditional physical training. The purpose of the study is to combine CrossFit training with the characteristics of basketball, arrange and design a targeted training program, and help athletes of the Guangdong University Basketball League to improve their physical fitness and performance on the basketball court through scientific training means and methods. Conclusion: Before the CrossFit training program, there is no significant difference in the physical fitness index scores of body shape, strength, speed, endurance, flexibility and sensitivity between the control group and the experimental group, There is no significant difference between the physical status of the control group and the experimental group before the CrossFit training program; After the CrossFit training program, there are significant differences between the control group and the experimental group in terms of body shape, strength, speed, endurance. There were no significant differences in flexibility and sensitivity, but the experimental group improved more than the control group. There is a significant difference between the physical status of the control group and the experimental group after the CrossFit training program; There is no significant difference in the physical status of the control group before and after the experiment. There is a significant difference in the physical status of the experimental group before and after CrossFit training. CrossFit training program is more suitable for improving the physical fitness of college basketball players in Guangdong Province.