To clarify the performance of functional microorganisms involved in biological citric acid wastewater treatment systems, bacterial community structure of anaerobic granular sludge was investigated in an internal circulation (IC) anaerobic reactor treating citric acid industry wastewater. Microstructure observation was carried out by environmental scanning electron microscope (ESEM), and the microbial diversity and microfloras were analyzed by high-throughput sequencing. Particle size distribution results showed that the most particles' diameters ranged from 1.0 mm to 4.0 mm (accounted for 74.4%). ESEM results showed that spherical bacteria were the dominant microorganisms in granular sludge. The total dataset comprised 8 397 high quality sequences, which could be subdivided into 873 operational taxonomic units. A library coverage of 0.936 implied that the granular sludge exhibited a high microbial diversity and abundance. The Shannon index, ACE index and Chao1 index were 4.376, 3 415.51 and 2 246.51, respectively. Genus classification revealed that there were four typical bacterial groups: hydrolytic fermentative bacteria for organic matter degradation were closely related to Paludibacter, Parabacteroides, Erysipelotrichaceae, Clostridium, Phascolarctobacterium, Aminobacterium, Saccharofermentans and Alkaliflexus, which accounted 24.93% of the bulk bacterial; H₂-producing and acetogenic bacteria were correlated with Petrimonas and Syntrophomonas, which accounted for 34.89%; methanogens of Methanosaeta accounted 3.44%; and the microflora groups of Levilinea, Longilinea and Thermovirga could be capable of tolerating toxic industrial wastewater, accounting for 14.62% instead.