Abstract: To explore the effects of three pepper varieties on bacterial taxa and quality of Zhaguangjiao, Zhaguangjiao prepared using Capsicum frutescens Linn., Capsicum annuum L., and Capsicum annuum L. var. grossum (L.) Sendt. for the test group, while two control groups without the addition of any vegetables and with the addition of only Apium graveolens var. rapaceum were set up, and based on that, the quality of Zhaguangjiao was digitally evaluated and its bacterial taxa were resolved by high-throughput sequencing. Finally, the correlations between Zhaguangjiao quality and dominant bacterial genera were revealed. It was found that, compared with Zhaguangjiao prepared using Capsicum frutescens Linn., both the bacterial diversity and abundance of Zhaguangjiao prepared using Capsicum annuum L. and Capsicum annuum L. var. grossum (L.) Sendt. were higher. Zhaguangjiao prepared using Capsicum annuum L. and Capsicum annuum L. var. grossum (L.) Sendt. were dominated by Lactobacillus with average relative abundances of 77.53% and 94.41%, respectively, while Zhaguangjiao prepared using Capsicum frutescens Linn. was dominated by Pseudomonas with an average relative abundance of 67.35%. Compared with Zhaguangjiao prepared using Capsicum frutescens Linn., the sourness and content of aromatic compounds of Zhaguangjiao prepared using Capsicum frutescens Linn. was dominated by Pseudomonas were significantly higher, while the contents of organic sulfides, terpenes and nitrogen oxides among volatile substances were significantly lower. After Pearson correlation analysis, it was found that elevating the abundance of Lactobacillus in the fermentation system of Zhaguangjiao could obviously suppress the undesirable flavor and improve the content of aroma substances in Zhaguangjiao. Zhaguangjiao is popular for its sour and spicy taste, due to Capsicum annuum L. var. grossum (L.) Sendt. is less spicy, choosing Capsicum annuum L. as the main raw material to produce Zhaguangjiao has a positive effect enhancing the overall quality of the product.