Use of low-cost biological methods for ammonia removal as partial nitrification has been attracted by many environmental engineering researchers in recent years.In this study the removal of ammonia in high concentration sewage based on both complete and partial nitrification with the different sub-cycles has been investigated in pilot-scale and the results were compared. Ammonia concentration in synthetic wastewater was about 900 mg-N/L and fixed and varible volume of reactor was 3 and 6 liter respectively to create a suitable hydraulic retention time of 1.05-1.55 days in the different cases. The results of ammonia, nitrite and nitrate measurements by spectrophotometer have shown that it is possible to achieve partial nitrification by controlling temperature, pH, and dissolved oxygen and having more sub-cycles. Ammonia specific oxidation rate was about 13 to 16 percent more in complete nitrification compared to partial nitrification and in this condition the percent of nitrite accumulation was reduced from 91 to 51 in 3 sub-cycles and from 81 to 30 in 1 sub-cycle. Furthermore, increase of sub-cycles number from 1 to 3 had significant effect on increasing ammonia specific oxidation rate from 29 to 32 percent in partial and full nitrification, respectively. Results of this study showed that this method will be used for high ammonia removal in side stream process in addition to low nitrite oxidation rate in partial nitrification as compared to complete nitrification