Objective To analyse the changes in blood ammonia (BA) of soldiers before and after anaerobic training and the relationship of BA and other biochemical indicators so as to determine the feasibility of BA as the marker of monitoring physical training in soldiers of CAPF. Methods Ninety soldiers of CAPF were randomly selected and divided into three groups and separate training modes of 100m-running, 400m-obstacle race and leapfrog. The changes in BA, blood lactic acid (Bla), serum creatine kinase (CK) and cell-free plasma DNA (cf-DNA) were determined before and after training in each group. Relationship of BA and other biochemical indicators was analysed and Pearson’s correlation coefficient was calculated. Results The baseline (pretraining level) of indexes in each group had no significant difference (P>0.05). Compared with pretraining value, BA, CK and cf-DNA increased (all P<0.01) but Bla had no significant change in 100 m-running group; all indexes rose in both 400m-obstacle group and leapfrog group (all P<0.01). Correlation analysis displayed that BA and CK, cf-DNA had significant positive correlation (P<0.05 and P<0.01 respectively) but no relation with Bla in 100 m-running group (P>0.05); BA and Bla, CK, cf-DNA had significant positive correlation in both 400m-obstacle group and leapfrog group (all P<0.01). Conclusions BA may be a convenient monitoring indicator in anaerobic training for soldiers.