Simultaneous removal of SO and NO from flue gas can be biologically achieved by the rotating drum biofilter with Fe(EDTA) as a solvent. One issue related with this process is the generation of HS. To control its generation, the pathways of HS formation were investigated, and the parametric tests were conducted. The addition of Fe(EDTA) (10 mM) increased the removal efficiency of NO and SO, while the S concentration decreased from 81 to 3.5 mM. The parametric tests showed that the high NO concentration favored the SO removal and significantly inhibited the HS generation. High-throughput sequencing showed that the dominant denitrifying bacteria were Pseudomonas (9.09%), and the main sulfate-reducing bacteria were Desulfovibrio (5.84%). The long-term operation confirmed that the system could effectively simultaneous perform biological denitrification and desulfurization, and the HS could be controlled.