The difference in microbiota was examined for breeders with different egg-laying rates, and the impact of dietary Enterococcus faecium (EF) was also determined in the present study. A total of 256 Arbor Acres broiler breeders (48-wk-old) were used in a 2 × 2 factorial design, which encompassed 2 egg-laying rate levels [average (average egg laying: AP, 80.45 ± 0.91%) and low (lower egg laying: LP, 70.61 ± 1.16%)] and 2 different dietary groups [control (no additive), 6 × 108 cfu/kg EF]. The results showed that the AP breeders presented a lower egg weight, feed conversion ratio, abdominal fat rate, and serum leptin level (P(laying) ≤ 0.05) as well as a higher egg-laying rate (P(laying) < 0.01) than the LP breeders. Dietary supplementation with EF improved the egg weight (P(EF) = 0.03) and had a higher concentration of follicle-stimulating hormone (FSH) in the serum (P(EF) = 0.04). The relative expression of Caspase 9, Bax, AMHR, BMP15, and GATA4 in the ovary of AP breeders was lower, whereas the FSHR and BMPR1B expression was higher than that measured in LP breeders (P(laying) ≤ 0.05). LP increased the abundance of Bacteroidetes (phylum), Firmicutes (phylum), Bacteroidia (class), Clostridia (class), Bacteroidales (order), Clostridiales (order), and Lachnospiraceae (family), whereas the AP promoted the enrichment of Proteobacteria (phylum) and Gammaproteobacteria (class) (P(laying) < 0.05). The genera Bacillus, Rhodanobacter, and Streptomyces were positively correlated with the egg-laying rate and BMPR1B expression (P < 0.05) but negatively correlated with the abdominal fat rate (P < 0.05) and Caspase 9 (P < 0.05). These findings indicate that the low reproductive performance breeders had lower microbiota diversity and higher Firmicutes, which triggers the energy storage that led to higher fat deposition. Besides, increases in the abdominal fat rate, leptin level, and apoptosis (Caspase 9, Bax) and reproduction-related gene (BMP15, AMHR, BMPR1B, and GATA4) expression would possibly be the potential mechanisms under which breeders have different reproductive performance. Dietary EF increased the egg weight and serum FSH level and decreased the Bacteroidetes (phylum) in low reproductive breeders.