The application of waste biomass-derived hydrochar to soil may cause extremely intensive nitrous oxide (N2O) fluxes that can challenge our current mechanistic understanding of the global nitrogen cycle in the biosphere. In this study, two waste biomasses were used to prepare cyanobacterial biomas-derived hydrochar (CHC) and wheat straw-derived hydrochar (SHC) for short-term incubation experiments to identify their effects and mechanisms of waste biomass-derived hydrochar on soil N2O efflux, with time-series samples collected for N2O efflux and soil analysis. The results showed that CHC and SHC caused short-term bursts of N2O effluxes without nitrogen inputs. Moreover, the enrichment of exogenous organics and nutrients at the hydrochar-soil interface was identified as the key factor for enhancing N2O fluxes, which stimulated microbial nitrification (i.e., increased gene copy number of ammonia oxidizing bacteria) and denitrification (i.e., increased gene copy number of nitrate and N2O reducing bacteria) processes. The concentrations of Fe (II) and hydroxyl radicals (HO•) were 6.49 and 5.63 times higher, respectively, in the hydrochar layer of CHC than SHC amendment. Furthermore, structural equation models demonstrated that HO•, as well as soil microbiomes, played an important role in driving N2O fluxes. Together, our findings provide a deeper insight into the assessment and prognosis of the short-term environmental risk arising from agricultural waste management in integrated agriculture. Further studies under practical field application conditions are warranted to verify the findings.