A lab-scale sequencing batch reactor (SBR) was setup and the aerobic granular sludge was successfully incubated by using anaerobic granular sludge as seed sludge. Nitrogen was partially removed by simultaneous nitrification and denitrification (SND) via nitrite with free ammonia (FA) of about 10 mg/L. The denaturing gradient gel electrophoresis (DGGE) method was used to investigate community structure of α-Proteobacteria, β-Proteobacteria, ammonia oxidizing bacteria (AOB), and Nitrospira populations during start-up. The population sizes of bacteria, AOB and Nitrospira were examined using real-time PCR method. The analysis of community structure and Shannon index showed that stable structure of AOB population was obtained at the day 35, while the communities of α-Proteobacteria, β-Proteobacteria, and Nitrospira became stable after day 45. At stable stage, the average cell densities were 1.1×1012, 2.2×1010 and 1.0×1010 cells/L for bacteria, AOB and Nitrospira, respectively. The relationship between characteristics of nitrifying bacteria community and nitrogenous substrate utilization constant was discussed by calculating Pearson correlation. Certain correlation seemed to exist between population size, biodiversity, and degradation constant. And the influence of population size might be greater than that of biodiversity.