The misuse and abuse of antibiotics in livestock and poultry seriously endanger both human health and the continuously healthy development of the livestock and poultry breeding industry. Plant-derived bioactive compounds (curcumin, capsaicin, quercetin, resveratrol, catechin, lignans, etc.) have been widely studied in recent years, due to their extensive pharmacological functions and biological activities, such as anti-inflammatory, antioxidant, antistress, antitumor, antiviral, lowering blood glucose and lipids, and improving insulin sensitivity. Numerous studies have demonstrated that plant-derived bioactive compounds are able to enhance the host's ability to resist or diminish diseases by regulating the abundance of its gut microbiota, achieving great potential as a substitute for antibiotics. Recent developments in both humans and animals have also highlighted the major contribution of gut microbiota to the host's nutrition, metabolism, immunity, and neurological functions. Changes in gut microbiota composition are closely related to the development of obesity and can lead to numerous metabolic diseases. Mounting evidence has also demonstrated that plant-derived bioactive compounds, especially curcumin, can improve intestinal barrier function by regulating intestinal flora. Furthermore, bioactive constituents can be also directly metabolized by intestinal flora and further produce bioactive metabolites by the interaction between the host and intestinal flora. This largely enhances the protective effect of bioactive compounds on the host intestinal and whole body health, indicating that the bidirectional regulation between bioactive compounds and intestinal flora has great application potential in maintaining the host's intestinal health and preventing or treating various diseases. This review mainly summarizes the latest research progress in the bioregulation between gut microbiota and plant-derived bioactive compounds, together with its application potential in humans and animals, so as to provide theoretical support for the application of plant-derived bioactive compounds as new feed additives and potential substitutes for antibiotics in the livestock and poultry breeding industry. Overall, based on this review, it can be concluded that plant-derived bioactive compounds, by modulating gut microbiota, hold great promise toward the healthy development of both humans and animal husbandry.