Immune system imbalance arises from a complex interplay of genetic, environmental, chronic disease, age, and emotional factors. It can lead to diseases including diabetes, obesity, atherosclerosis, and cancer, representing a critical threat to human health. Food-derived bioactive peptides possess immunomodulatory properties. As safe food resources, they are characterized by multi-targeting and high consumer acceptability. This review primarily focuses on the preparation technologies, structural analysis, structure-activity relationships, and mechanisms of bioactive peptides derived from food sources. Furthermore, current achievements are summarized in the field of immunomodulation by the peptides, while perspectives are offered.