This study examined the correlation between non-metallic organic tanning agents (NOTAs) and wastewater containing double-triazine (bistriazine). Specifically, high-throughput sequencing was used to analyze how the physical and chemical properties of the bistriazine-containing wastewater affected the microbial community. In total, 9995 operating taxonomy units (OTUs) were detected at a similarity level of 97%. According to the taxonomy results and relative bacterial richness, the non-metallic organic tanning agent (NOTA) wastewater communities showed significant differences. Clostridium sensu stricto and Turicibacter bacteria were dominant in NOTA T2, T3, and the blank control (KB) wastewater; Trichococcus and Aeromonas were dominant in NOTA T4; and Pseudomonas was dominant in T2, T4, and the blank control (KB). Thus, the addition of bistriazine ring derivatives altered the composition of the bacterial community. Furthermore, Spearman’s correlation analysis revealed a substantial correlation in the composition of the communities and the physicochemical properties of the wastewater. Acidocella and norank c Cyanobacteria correlated positively with Total Phosphorus (TP) (p ≤ 0.001) and Mycobacterium showed a positively held correlation with pH (p ≤ 0.05). Conversely, norank_f__Elev-16S-1332 indicated a negative correlation with TP, Total Nitrogen (TN), and Total Organic Carbon (TOC) (p ≤ 0.05), whereas Zoogloea correlated negatively with NH3–N, TOC, and TN (p ≤ 0.05). Regarding water quality, a significant correlation between microbial communities and the physicochemical properties of bistriazine wastewater was also observed (p ≤ 0.05). We concluded that Trichococcus, Clostridium sensu stricto, Turicibacter, Pseudomonas, Intestinibacter, Acidocella, Bacillus, and Tolumonas showed a high tolerance for bistriazine wastewater, which could offer insight into its bioremediation.