The distinctive geographical environment of the Qinghai–Tibet Plateau has nurtured a variety of anthocyanin-rich berry plants. This review systematically summarizes the current state of research on anthocyanins obtained from Lycium ruthenicum Murr. (LRAs), Nitraria tangutorun Bobr (NTAs), and Rubus idaeus (RAs) for their potential health benefits and use. The anthocyanins found in these three berries have attracted considerable interest for their significant biological effects, such as their antioxidant, anti-aging, hypoglycemic, anti-inflammatory, and neuroprotective activities, as well as their ability to regulate the gut microbiota and inhibit cancer cells. These anthocyanins have potential applications as natural colorants, packaging materials and smart labels, as well as functional food and health supplements in the food industry. They have diverse molecular architectures with glycosylation and acylation profiles. The structural features of anthocyanins are closely related to their biological activities. This review provides a detailed overview of the chemical structures, synthesis pathways, biological activities, and applications in the food industry of LRAs, NTAs, and RAs. This summary offers a theoretical foundation for exploring plant resources characteristic of the Qinghai–Tibet Plateau and for the development and utilization of high-value-added functional foods, pharmaceuticals, and cosmetics.