The microbial community and extracellular polymeric substances composition of anaerobic granular sludge exposed to selenate (~10mg/L), cadmium (Cd) and zinc (Zn) (~2 and 5mg/L) were investigated by high-throughput sequencing and fluorescence excitation emission matrix (FEEM) spectra, respectively. As a response to selenate, Cd and/or Zn exposure, significant fluorescence quenching of fulvic-like acids and humic-like substances was observed. With selenate, Cd and/or Zn in the influent with respective concentrations of 10, 5 and 5mg/L, the abundance of the phyla Proteobacteria, Firmicutes, Spirochaetae, Cloacimonetes and Synergistetes increased significantly, and the dominant taxa in the anaerobic granular sludge exposed to Se, Cd and/or Zn were Halothiobacillaceae (10.2%), Pseudomonas (8.8%), Synergistaceae (7.7%), Spirochaetaceae (7.2%), Blvii28 wastewater sludge group (6.7%), Telmatospirillum (4.6%), Veillonellaceae (4.3%), Geobacter (4.0%) and Enterobacteriaceae (3.0%). Compared with the inoculum, the abundance of the archaea Methanobacterium and Methanosaeta decreased to below detection limit in the UASB reactor after 116 days exposure to Se, Cd and Zn.