As the second largest greenhouse gas, methane production and emission have great effect on global warming and carbon cycle in the ecosystem. Paddy soil is one of the main sources of atmospheric methane. Urea fertilizer which affects yield and quality of rice plays an important role in regulation methane emission flux. In order to study the effect of urea fertilizer on methane production and methanogenic archaeal community structure at different temperatures, the neutral paddy soils were incubated under anaerobic condition with urea of 0 and N 400 mg/kg at 15℃, 25℃, 37℃ and 50℃ for 100 days. The cumulant of methane-production and soil characteristics such as pH, organic carbon and nitrogen of ammonium were detected during the incubation. The shifts of methanogenic archaeal community structure with incubation time in different treatments were analyzed by terminal restriction fragment length polymorphism (T-RFLP) analysis based on archaeal 16S ribosomal RNA gene. The results showed that urea fertilizer inhibited methane production in paddy soil at low or medium temperature (15℃ – 37℃), while had no effect on the accumulated methane production at high temperature (50℃). Urea may influence methane production by altering the community structure of methane-producing archaea. Urea fertilizer decreased the stability and increased the diversity of methanogenic archaeal community structure with incubation time in the range from 15℃ to 37℃. But there was unconspicuous influence of urea fertilizer on methanogenic archaeal community structure at 50℃. The result of T-RFLP indicated that urea reduced the relative abundance of Methanosarcinaceae under these four experimental temperatures. Urea prossibly had nothing to do with the changes of methane-producing mechanism as temperature changed.