The effect of anaerobic activated sludge (AS) and granular sludge (GS) as inoculum on methane production (MP) with different ammonia levels was compared. About 35% of MP loss was observed when the ammonia level exceeded 3 g of NH4+ N/L in AS reactors and 5 g of NH4+ N/L in GS reactors. Propionate accumulation in GS reactors was 66-80% lower than that in AS reactors when the ammonium concentration was higher than 3 g of NH4+ N/L. Nevertheless, lactate appeared to be an important intermediate product in GS reactors under a high ammonia level. The ammonia impact on GS was further discussed. Under a high ammonium concentration, the loss of an extracellular polymeric substance, the increase of zeta potential, and the cracked surface indicated a negative effect on the granular structure, while a blank center, as illustrated by fluorescent in situ hybridization, also suggested the collapse potential of zooglea. With 16S rRNA analysis, obvious differences appeared on the archaeal community on each ammonium concentration.