Objective To assess the effect of yoga exercise training on the physical and mental qualities of students in military universities. Methods According to the newly issued Physical Standards for Soldiers, we chose 60 naval general practice students (age 18-22 years) for this study and they were divided into test group (n=30) and control group (n=30). The test group undertook yoga exercise once a week (two hours each time) for 10 weeks in addition to ordinary military exercises; the control group only undertook ordinary military exercise. The height, body mass, body mass index (BMI), fat rate, basal metabolic rate (bioelectrical impedance), flexibility (forward split, cross split and stand trunk bending), and anxiety level (internationally acknowledged Self-Rating Anxiety Scale \[SAS\]) were determined and compared between the two groups before and after training. And the effect of yoga exercise on the physical and mental qualities of students was analyzed. Results After ten weeks’ of training, the SAS scores were significantly decreased in both groups (P<0.01), and that of the test group was significantly lower than that of the control group (P<0.01). The BMI and fat rate were significantly decreased in the two groups after training (P<0.01) and the test group had a better body flexibility than the control group. Conclusion Yoga exercise training can help to relieve mental pressure and improve the overall physical and mental qualities of students in military universities, and it is feasible to popularize it in military academies.