The filling substrate is one of key factors influencing effectiveness of sulfate reducing packed-bed bioreactor (SRPB) treating acid mine drainage (AMD). The effects of four substrates (i.e. quartz sand, steel residue, biochar, and peanut shell) on remediation performance and sulfur transformation of SRPB treating AMD was studied. The results showed that steel residue and biochar improved sulfate reduction efficiency (61% and 49%) compared to quartz sand (32%), whereas peanut shell inhibited sulfate reduction efficiency (19%), attributed to its decomposition process leading to a severe accumulation of acetic acid. More amounts of sulfides generated in steel residue bioreactor were converted into acid volatile sulfide and elemental sulfur, resulting in a significant decrease in dissolved sulfide in the effluent. Metals (Fe, Al, Zn, Cd and Cr) except for Mn were effectively immobilized in the bioreactors, particularly for Al and Cd. Sulfate reducing bacteria and sulfide oxidizing bacteria lived symbiotically in all bioreactors which exhibited similar heterogeneity in microbial distribution and function, i.e. bacterial sulfate reduction mainly occurring in bottom-middle layers and photoautotrophic sulfide oxidation in upper layer close to outlet. The microbial response mechanism to various substrate environments was revealed through co-occurrence networks analysis. This study suggests that attention should be paid to the inhibitory effect of acetic acid accumulation on sulfate reduction when using sole lignocellulosic waste (peanut shell), and steel residue and biochar could be utilized as filling substances to promote sulfate reduction.