With economic development and social progress, consumers are paying more and more attention to food safety and quality. Traditional packaging techniques are difficult to monitor food quality in real time. Therefore, intelligent packaging technologies represented by freshness indicator films have emerged. Bioactive compounds, due to their degradability, antioxidant properties and biosafety, have become the core materials for constructing green and intelligent indicator films. This article systematically reviews the application and challenges of bioactive substances in food intelligent indicator films. It is found that nanocellulose has high loading and response characteristics, along with the dual advantages of preserving the bioactivity of encapsulated substances and providing favorable loading performance for lipophilic compounds. Chemical modification can endow cellulose derivative substrates with excellent water or organic solubility, making them easy to form films. Polysaccharide materials can not only provide structural support and load platforms, but also achieve intelligent responses by responding to environmental stimuli. Protein-based degradable materials can be used to prepare hydrophilic or hydrophobic property indicator films and applied in various foods. Flavonoids, phenols and quinone pigments in natural indicators can achieve the effect of preservation and monitoring through color changes in different pH environments by being compounded with other materials. Real-time monitoring of the freshness of meat, seafood, fruits, vegetables and dairy products can be achieved by utilizing the color reaction between different spoilage and deterioration signals and indicator films. Future research should focus on developing high-performance carriers and more stable indicators to expand the application scenarios of intelligent indicator films, thereby achieving purer, more efficient and stable green packaging applications.