Heterotrophic-autotrophic denitrification reduces the cost of wastewater treatment and the risk of excess chemical oxygen demanded (COD) in the effluent. A mixotrophic denitrification system involving mixed heterotrophic and ferrous autotrophic bacteria was investigated to treat low-C/N ratio (C/N, defined as chemical oxygen demand (COD)/total nitrogen (TN)) wastewater with pyrite and organic carbon as electron donors. The system yielded effluent total nitrogen (TN) of 0.38 mg/L in 48 h due to a synergistic effect when the C/N ratio was 0.5 and influent nitrate nitrogen (NO3−-N) was 20 mg/L; this TN value was significantly lower than those of the heterotrophic system (14.08 mg/L) and ferrous autotrophic system (12.00 mg/L). The highest abundance of the narG gene was observed in the mixotrophic denitrification system, along with more abundant microbial species. The dominant denitrification bacteria in each system included Thaurea, Ferritrophicum, Pseudomonas, and Thiobacillus, which varied with the initial inoculum source and the environment. Nevertheless, the abundance of the heterotrophic bacteria Thaurea decreased with prolonged operation of the systems. Together, these results implied that the simultaneous heterotrophic and FeS2-based ferrous autotrophic denitrification process can be an alternative approach for the treatment of low-C/N ratio wastewater.