An integrated reactor system was developed for the simultaneous removal of carbon, sulfur and nitrogen from sulfate-laden wastewater and for elemental sulfur (S0) reclamation. The system mainly consisted of an expanded granular sludge bed (EGSB) for sulfate reduction and organic carbon removal (SR-CR), an EGSB for denitrifying sulfide removal (DSR), a biological aerated filter for nitrification and a sedimentation tank for sulfur reclamation. This work investigated the influence of chemical oxygen demand (COD)/sulfate ratios on the performance of the system. Influent sulfate and ammonium were fixed to the level of 600 mg SO42− L−1 and 120 mg NH4+ L−1, respectively. Lactate was introduced to generate COD/SO42− = 0.5:1, 1:1, 1.5:1, 2:1, 3:1, 3.5:1 and 4:1. The experimental results indicated that sulfate could be efficiently reduced in the SR-CR unit when the COD/SO42− ratio was between 1:1 and 3:1, and sulfate reduction was inhibited by the growth of methanogenic bacteria when the COD/SO42− ratio was between 3.5:1 and 4:1. Meanwhile, the Org-C/S2−/NO3− ratios affected the S0 reclamation efficiency in the DSR unit. When the influent COD/SO42− ratio was between 1:1 and 3:1, appropriate Org-C/S2−/NO3− ratios could be achieved to obtain a maximum S0 recovery in the DSR unit. For the microbial community of the SR-CR unit at different COD/SO42− ratios, 16S rRNA gene-based high throughput Illumina MiSeq sequencing was used to analyze the diversity and potential function of the dominant species.