Objective To investigate the effects of ambroxol hydrochloride on surface structure of trachea mucosa in rats injured by intratracheally instilled amikacin. Methods Thirty Wistar rats injured by intratracheally instilled amikacin ( 0. 252 mL/kg) were randomly divided into a control group ( n =15) and an ambroxol group ( n= 15) . The rats in the ambroxol group were intraperitoneally injected with ambroxol hydrochloride ( 70 mg/kg) 5 minutes after amikacin administration. They were all equally divided into five subgroups and sacrificed at 2, 4, 8, 28, 48 hours respectively. Then the samples of 1/3 lower segment of trachea were collected and observed under scanning electron microscope. Results In the control group, the mucous secretion and its stickness were increased. The cilia were found lodged, sticked together, aligned abnormally, abrupt partly, and recovered slowly, with the percentage of damaged area of 98. 2% , 98. 5% , 97. 5%, 92. 7% , 82. 1% at 2, 4, 8,24,48 h, respectively. The injuries of mucosa in the ambroxol group were much milder and recovered more rapidly than those in the control group, with the percentage of damaged area of 85. 7% , 81. 9% , 73. 0% , 61. 9% , 50. 2% at 2, 4, 8, 24, 48 h, respectively. Conclusions Intratracheal instillation of amikacin can cause cilia ultrastructure damage on tracheal mucosa. Ambroxol can promote the recovery process and alleviate airway inflammation.