A complex dynamic equilibrium exists between gut microbes and the male host, whose composition, abundance, metabolites, and signaling pathways significantly influence physiological functions from the local gut to distal organs such as the testes, kidneys, and parasympathetic gonads, thereby modulating host semen quality. The intestinal flora can influence animal semen quality by regulating both metabolic substrates (short-chain fatty acids, amino acids, vitamins) and androgen metabolism, but also release signaling molecules (Serotonin, gamma-aminobutyric acid, nitric oxide and hydrogen sulfide ) to regulate male reproductive function. This paper reviews the research progress on the effects of gut microbes on semen quality and reproductive performance of animals, aiming to provide a theoretical reference for improving animal semen quality.