Phenols are natural compounds with considerable bioactivities. However, the low bioavailability and chemical instability of phenols limit their biological functions. This review summarizes recent progress in phenol delivery systems that account for the specific physiological conditions of the gastrointestinal tract. It focuses on the delivery materials for intestinal targeting and the synergistic benefits of co-encapsulating phenols with other functional ingredients. To achieve targeted release of phenols in the digestive tract, factors such as pH, digestive enzymes, and gut microbiota should be fully considered in delivery system designing. Materials like chitosan, sodium alginate, pectin, and guar gum offer effective protection and targeted delivery of phenols due to their pH sensitivity and enzyme-degradable properties. Co-delivery systems that combine phenols with carotenoids or probiotics improve the functional properties of phenols, such as antioxidant activity, anti-inflammatory effect, and regulation of gut microbiota. Probiotics can enhance phenolic compound absorption and probiotic survival in a phenolic-probiotic co-encapsulation system through debonding, bioconversion, and synergistic effects.