The effects of the novel biological inhibitor cyclopenten-one (CCO) on nitrous oxide (N2O) emission in different soils were compared，aiming to investigate the inhibiting mechanism. In this study，two typical agriculture soils(red soil in Jiangxi and irrigated desert soil in Gansu)were collected and used in the incubation experiment in the condition of 25℃ and 60% water filled pore space. There were three treatments treated as no urea control (CK)，adding urea (U) and adding CCO in urea (U+CCO)，respectively. The results showed that the use of CCO prolonged existing of NH4+-N in both two different soils and reduced nitrification potential. The N2O emission was reduced 74.12%(red soil) and 63.19%(irrigated desert soil) by adding CCO in red soil and irrigated desert soil，respectively，compared to the urea treated soil. The real-time PCR results showed that the utilization of urea improved soil ammonia oxidizers’ activity. The effects of inhibition of CCO on ammonia oxidizing bacteria amoA gene abundance in irrigated desert soil (85.81%) was better than that in red soil (19.63%)，while it was no significant inhibitory effect on ammonia oxidizing archaea. In the meantime，the activity of nirS and nirK gene activity was promoted by the utilization of CCO. The inhibition effect on anti digestion functional gene nirS and nirK appeared on the 7th day of cultivation in red soil，while it appeared on the 25th day in irrigated desert soil. Overall，CCO could inhibit nitrification and denitrification process in red soil and irrigated desert soil by decreasing the activity of nitrification/denitrification functional genes so that reduced the emission of N2O.