Objective To explore the significance of functional training of core muscles for preventing low back pain and improving core muscle function in recruits. Methods Healthy male recruits were enrolled from a naval training base and were randomly assigned to core muscle training group and conventional lumbar muscle training group. The recruits in the two groups received functional training of core muscles and routine training of lumbar and abdominal muscles for 12 weeks, respectively. The training procedure was 3-5 times a week and increased with training cycle, with 3 sets of actions being completed every time for 30 min. On the 4^th, 8^th and 12^th weeks, rehabilitation physicians came into the base and investigated the incidence of low back pain of the recruits. Two fixed physicians carried out waist core muscle stability bridge test and waist and back core muscle endurance test on the 1^st and 12^th weeks. Results Totally 588 recruits were enrolled, including 295 recruits in the core muscle training group and 293 in the conventional lumbar muscle training group. The incidence of low back pain on the 12^th week was significantly lower in the core muscle training group than that in the conventional lumbar muscle training group (1.13%[3/266] vs 6.07%[15/247], P=0.002). On the 12^th week, the bridge and endurance of lumbar muscles were significantly increased versus those on the 1^st week in the two groups, but the growth rate of the core muscle training group was significantly greater than that of the conventional lumbar muscle training group (all P<0.01). Conclusion Compared with traditional lumbar muscle training, functional training of core muscles more effectively prevents low back pain, enhances the lumbar and abdominal core muscle to maintain spinal stability, and improves back muscle endurance.