In order to investigate the treatment efficiency of ammonia nitrogen and nitrite nitrogen by different pH values and filter material, we collected nitrifying bacteria in the intensive recirculating aquaculture system as the research object to study the effects of ammonia elimination of six pH gradient (pH 5.0-10.0) and four filter material (ceramic ring, corallite, biofilters brush, biology-ball). When the pH was 8.0-9.0, the removal rate of ammonia nitrogen was 99.86% and 98.95% respectively, which was high than pH 6.0（66.18%）, pH 7.0（71.43%）and pH 10.0（70.51%）. The increase of nitrite nitrogen was less than the decline of ammonia nitrogen when pH was 7.0-9.0, and the great difference appeared at pH 9.0. In the filter material experiment, we found that the removal rate reaching 100% of ammonia nitrogen by biofilters brush, ceramic ring, corallite and biology-ball was on day 3, 4, 6, 7 respectively. The concentration of nitrite nitrogen of ceramic ring and corallite had gradually declined when they reached their highest level 9.60 mg/L and 10.00 mg/L respectively. The concentration of nitrite nitrogen of biofilters brush and biology-ball was maintain a high level when they reached their highest level 9.55 mg/L and 11.00mg/L respectively. The results show that nitrifying bacteria are suitable for alkaline condition(pH 8.0-9.0), especially at pH 9.0. Different filtration materials have different effects on ammonia nitrogen and nitrite nitrogen. Ceramic ring has the better removal rate of ammonia nitrogen and nitrite nitrogen than the other filter material. Biofilters brush only has a good removal effect on ammonia nitrogen. Corallite only has a good removal effect on nitrite nitrogen. Various filter material use would improve the treatment effect of the nitrifying bacteria.