Thymol is a naturally occurring volatile terpenoid in plants that possesses strong antifungal activities against many pathogens. In this research, thymol was included into β-cyclodextrin and the antifungal activity of the resulting complex against Geotrichum citri-aurantii, the causal agent of sour rot in citrus fruit, was investigated. The inhibition concentration of the β-cyclodextrin-thymol inclusion complex (β-CTIC) to G. citri-aurantii was estimated to be 4.0 g L−1, which was supposed to be a comparable antifungal efficiency of 0.5 g L−1 thymol alone. The structure and characteristic of β-CTIC were evaluated by scanning electron microscopy (SEM), X-ray diffraction (XRD), nuclear magnetic resonance (NMR) and entrapment efficiency (EE). The ROESY spectrum of β-CTIC showed appreciable correlation of H-1, H-4 and H-3 protons of thymol with the H-3′, H-5′ and H-6′ protons of β-cyclodextrin, respectively. In addition, β-CTIC was found to reduce the decay of citrus fruit inoculated with G. citri-aurantii and maintain the fruit quality. Our present study suggested that β-CTIC might be used as an alternative to chemical fungicides in controlling the postharvest sour rot of citrus fruit.