Composting is employed as an important treatment for livestock manure. Unfortunately, large amounts of nitrogen are lost mainly via NH₃ and N₂O emissions during composting, causing severe environmental contamination. The application of additives is a highly effective strategy for decreasing their releases during composting. In this study, the effects of adding microbial agents (lignocellulose-degrading microorganisms, LDM) and combined application of phosphogypsum and medical stone (PPM) on NH₃ and N₂O emissions and their underlying mechanisms during composting were explored. Results showed that LDM and PPM reduced 25.9% and 68.4% of NH₃ emissions and 35.0% and 42.9% of N₂O emissions, respectively. LDM and PPM had strong correlations with nirS-, nirK-, and nosZ-dominated denitrification processes with low abundance and LDM also reduced the abundance of nitrifying bacteria (amoA), which was significantly positively correlated with N₂O emission (P < 0.01). Furthermore, Firmicutes probably contributed to the transformation and release of nitrogen in thermophilic period, whereas Proteobacteria, Chloroflexi, and Bacteroidetes might play important roles in cooling and maturation periods. Structural equation modelling further demonstrated that the reduction in N₂O emission under LDM was related to the lower accumulation of NO₃^--N utilized by denitrifying microorganisms during maturation period. Network and redundancy analysis showed PPM mainly obtained lower NH₃ and N₂O emissions through the regulation of environmental variables, nitrogen functional genes and bacterial communities. Overall, these results offer insights at a molecular level into the effects of LDM and PPM on NH₃ and N₂O emissions during composting and provide theoretical and technical support for reducing NH₃ and N₂O emissions and environmental pollution.