<p>In recent years, natural pigments have made significant contributions to food preservation, antioxidant, and antibacterial fields due to a wide range of sources, high safety, and no obvious side effects, and are increasingly used as sensors and indicators for judging food freshness because of their unique chemical structures and physicochemical properties. This paper takes the latest research progress on natural pigments as indicators in the food industry as its starting point, providing a comprehensive review of the structure, types, freshness indicators, and functional characteristics of natural pigments as antioxidants and antimicrobial agents. The paper also explores the synergistic and antagonistic effects between different natural pigments, as well as the combined use of natural pigments with nanomaterials to enhance the stability of natural pigments in food industry applications. In addition, in order to actively respond to sustainable development, this review also describes the extraction of natural pigments from food waste and their application in the food industry. Finally, we summarize the advantages and challenges of natural pigments and look forward to the potential and future research prospects of pigments in interdisciplinary fields such as food and biomedicine, including the development of novel drug delivery systems.</p>