The purposes of this study were to investigate the possibility to apply ammonia stripping process with diffused air method for the removal of the highly concentrated ammonia nitrogen in wastewater from hexane fermentation process and to suggest optimal operating conditions of ammonia stripping process in the consideration of treatment cost and efficiency of treatment according to operation conditions. In pH control process that was applied as a pre treatment process of ammonia stripping, use of Ca(OH)2 was very effective not only to increase pH but also to remove CODCr, T-N, T-P, turbidity and color. The optimal pH of ammonia stripping was 10/5. The reaction time to satisfy 1,000 mg NH3-N/L was 2.6, 1.6, 0.8, 0.6 hrs at 25, 35, 45 and 55℃, respectively, at the air flow rate of 20L/min. CaCO3 removal process was required after ammonia stripping since the effluent contained high concentration of CaCO3 which were produced during aeration. Capital cost and operating cost also were decreased with the increased reaction temperature and air input. In conclusion, the ammonia stripping procedure was very efficient for the treatment of highly concentrated nitrogen in wastewater from hexane fermentation process and the optimal conditions of ammonia stripping were at the pH of 10.5, the temperature of 55℃, and the air flow rate of 20L/min.