The safety and quality of fruit after harvest has always been an issue of people’s livelihood. Due to increasing concerns about food safety and environmental pollution caused by excessive application of fungicides, there is a growing interest in the exploitation of antifungal bio-source substances. Therefore, it has been the focus of postharvest pathology to reveal the mode of the action and the effect on disease prevention of these antifungal bio-source substances. In recent years, some new bio-source substances have been explored that have enormous potential in postharvest disease control in various fruits, and their mechanisms against fungal pathogens have also become understood. This review will focus on recent advances in the mechanisms and applications of these bio-source substances for suppressing fungal pathogens and maintaining intrinsic quality of fruits. Moreover, further research hotspots and development directions are also proposed.