Although studies have reported on the preparation of composite films and its application, the preparation and application for fruit preservation of composite film with fennel seed essential oil (FEO) are unknown. In this study, six types of composite films (F1–F6) were prepared with chitosan/FEO/starch sodium octenyl succinate (SSOS). The physicochemical, antifungal and preservation properties were investigated. The water content, water vapor permeability and elongation at break of the films increased with the glycerol, but the density and tensile strength decreased. Fourier infrared spectroscopy showed that there was a hydrogen bond existed between the film components. The film surface was smoother with higher content of FEO and glycerin. The films exhibited strong antifungal activity against Botrytis cinerea, Trichothecium roseum, and Penicillium expansum. Among them F3, SSOS/glycerol/FEO/chitosan was 1:0.2:1:0.5, had the best antifungal performance. The F3 coating also reduced the lesion diameter of apple fruit inoculated with the three fungi. The F3 coating decreased respiration rate and weight loss, and maintained the firmness and peel lightness of fruit during storage. The findings of this work provide a new insight for exploration of composite film with fennel seed essential oil and its application for fruit preservation.