Blue mold decay is the most common disease during postharvest storage of apples caused by Penicillium expansum, leading to huge economic losses to the apple industry. Antagonistic yeasts are widely used in biological control, and organic compounds can be used as elicitors to induce antagonistic yeasts to further improve their biocontrol effect. In this study, we assessed the biocontrol efficacy of the antagonistic yeast, Debaryomyces hansenii, enhanced by alginate oligosaccharide (AOS) in controlling the postharvest decay of apples and studied the possible physiological mechanisms involved in this process. The results of this study were as follows: (1) AOS enhanced the biocontrol ability of D. hansenii against P. expansum infestation of apples. In the in vivo experiments, D. hansenii induced by 0.5% AOS significantly reduced the disease incidence and lesion diameter in apples, demonstrating good control of blue mold. When treated with D. hansenii-induced with AOS, the disease incidence rate of apples was only 21.6%, while that of yeast alone was 37.5%. (2) In the in vitro experiments, AOS significantly improved the inhibitory effect of D. hansenii on the germination rate, germ tube length, and colony diameter of P. expansum. The results suggested that AOS-induced yeast exhibited a certain inhibitory effect on the growth of P. expansum. (3) The activities of diseases resistance-related enzymes of apples treated with AOS-induced D. hansenii such as polyphenol oxidase (PPO), peroxidase (POD), and phenylalanine ammonia-lyase (PAL) were increased compared to the yeast alone and the control group. Apart from that, the content of substances such as total phenols and flavonoids maintained the original level. These results suggest that the resistance of apples against pathogenic fungi may be improved by increasing the activities of disease resistance related enzymes activities of the fruit. In summary, the method of enhancing antagonistic yeast by AOS is very promising and efficient for improving biological control to reduce economic losses in the apple industry.