Zearalenone (ZEN) is a ubiquitous contaminant in poultry feed, since ZEN and its metabolites can interfere with estrogen function and affect the reproductive ability of animals. The estrogen-like effect of ZEN on mammal is widely reported, while little information is available, regarding the effect of relatively low dose of ZEN on estrogen function and production performance of laying hens, and the relationship between them. This work was aimed to investigate the effects of ZEN on the production performance, egg quality, ovarian function and gut microbiota of laying hens. A total of 96 Hy-line brown laying hens aged 25-week were randomly divided into 3 groups including basal diet group (BD group), basal diet supplemented with 250 μg/kg (250 μg/kg ZEN group) and 750 μg/kg (750 μg/kg ZEN group) ZEN group. Here, 750 μg/kg ZEN resulted in a significant increase in the feed conversion ratio (FCR) (g feed/g egg) (p < 0.05), a decrease in the egg production (p > 0.05), albumen height and Haugh unit (p > 0.05), compared to the BD group. The serum Follicle-stimulating hormone (FSH) levels significantly decreased in ZEN supplemented groups (p < 0.05). Serum Luteinizing hormone (LH) and Progesterone (P) levels in the 750 μg/kg ZEN group were significantly lower than those in the BD group (p < 0.05). 16S rRNA sequencing indicated that ZEN reduced cecum microbial diversity (p < 0.05) and altered gut microbiota composition. In contrast to 250 μg/kg ZEN, 750 μg/kg ZEN had more dramatic effects on the gut microbiota function. Spearman’s correlation analysis revealed negative correlations between the dominant bacteria of the 750 μg/kg ZEN group and the production performance, egg quality and ovarian function of hens. Overall, ZEN was shown to exert a detrimental effect on production performance, egg quality and ovarian function of laying hens in this study. Moreover, alterations in the composition and function of the gut microbiota induced by ZEN may be involved in the adverse effects of ZEN on laying hens.