The human body relies on the intake and utilization of nutrients from food to support growth, development, and daily activities. However, certain groups, such as infants, the elderly, and patients with digestive diseases (e.g., chronic atrophic gastritis, pancreatitis, and cystic fibrosis) experience impaired gastrointestinal function due to developmental immaturity or physiological decline, leading to reduced digestion and absorption capacity. This has resulted in the emergence of pre-digested foods. Nonetheless, research on the nutritional and functional properties of these foods, specifically tailored to the gastrointestinal characteristics of these special populations, remains limited. This review begins with an overview of the general processes of digestion, absorption, and fermentation in the human digestive tract. It then summarizes the physiological characteristics of the gastrointestinal systems in infants, the elderly, and individuals with digestive diseases, while highlighting recent advancements regarding the effects of food pre-digestion on the digestive and absorption capabilities of these groups. The insights presented aim to provide a scientific foundation for the precise design and development of healthy foods suited for these populations.