This study reported for the first time that hyperthermophilic composting (HTC) could mitigate 90% of the cumulative amount of N2O emissions compared to traditional composting (TC) in a full-scale experiment. The concentrations of NO2--N and NO3--N in HTC were significantly lower than those in TC, which may be the main reason for the reduced N2O emissions. Furthermore, this study found that the decrease in N2O emissions in HTC compared to TC was mainly due to the inhibition of the abundance of the bacterial amoA and norB genes, which could decrease the nitrification rate and control N2O formation, respectively. Partial least squares path modeling revealed that a high temperature was the key factor in lowering N2O emissions in HTC, while physicochemical properties were the dominant factor in enhancing N2O emissions in TC. These results suggested that HTC is a promising technique for reducing N2O emissions in manure composting.