The aim of this study was to develop a simple operation strategy for the cultivation of partial nitrification granules (PNGs) treating an autotrophic medium. For this strategy, aerobic granular sludge adapted to high concentration organics removal was seeded in a sequencing batch reactor (SBR) with a height/diameter ratio of 3.8, and the ratio of organics to the ammonia nitrogen-loading rate (C/N ratio) in the influent was employed as the main control parameter to start up the partial nitrification process. After 86 days of operation, the nitrite accumulation rate reached 1.44 kg/(m(3) day) in the SBR, and the removal efficiency of ammonia nitrogen (NH4 (+)-N) was over 95 %. The PNGs showed a dense and compact structure, with an excellent settling ability, a typical extracellular polymeric substance (EPS) composition, and a high ammonia oxidation activity. The high-throughput pyrosequencing results indicated that the microbial community structure in the granules was significantly influenced by the C/N ratio, and ammonia-oxidizing bacteria (AOB), including the r-strategist Nitrosomonas and k-strategist Nitrosospira genre, which accounted for approximately 40 % of the total biomass at the end of operation. The effective suppression of nitrite-oxidizing bacteria (NOB) growth was attributed to oxygen competition on the granular surface among functional bacteria, as well as the high free ammonia or free nitrous acid concentrations during the aeration period.