A modified sequencing batch reactor, which adds a pre-anoxic phase before the aeration phase, was used to treat toxic landfill leachate, and high-throughput sequencing technology used to study how the classification, distribution and abundance of functional bacterial communities varies during system operation. The system operation results are as follows: in the full load steady operation period (II), influent/effluent chemical oxygen demand (COD) and total nitrogen (TN) concentrations were approximately 6,421/645 and 1,210/19 mg/L, respectively; TN and COD removal rates of the system were above 93% and 87%, respectively. The bacterial community structure of the system is as follows: when compared with the bacterial community structure of the inoculation sludge, the final dominant phyla of the system were Proteobacteria (49.4%) and Bacteroidetes (36.5%), while beta-Proteobacteria (30.05%) and alpha-Proteobacteria (16.4%) under Proteobacteria were the two dominant classes in the full load steady operation period (II). Nitrosomonas (22.56%) was the main ammonia-oxidizing bacteria within beta-Proteobacteria. The bacterial community associated with endogenous denitrification included Paracoccus (alpha-Proteobacteria, 19.15%), Thauera (beta-Proteobacteria, 8.36%), and Truepera (4.96%). Paracoccus and Thauera were endogenous denitrifying bacteria that could transform organic matter into polyhydroxyalkanoates (PHA) and use PHA to remove nitrogen under anaerobic conditions, and Truepera could resist leachate toxicity.