This study aimed to enhance the antioxidant activity, antifungal activity, and oxidation stability of Citrus reticulata essential oil (EO) nanocapsules by using cinnamon EO and clove EO. The encapsulation efficiency, moisture content, water activity, particle properties, glass transition temperatures, relative crystallinity, and chemical structure were analyzed. Results showed that all formulas have stable moisture levels (less than 6%), water activity (less than 0.6), and an encapsulation efficiency higher than 91%, which were confirmed by the Fourier transform infrared spectroscopy results. Compared with C. reticulata EO (CEO), the addition of cinnamon EO and clove EO increased the total phenolic content by 1.75 and 1.54 times, respectively. The results indicated that the addition of cinnamon EO and clove EO increased the antioxidant activity by 3.57 and 2.08 times, as well as increased the antioxidant capacity by 4.43 and 3.52 times, respectively. The antifungal efficacy of CEO nanocapsules was enhanced by 3.13, 1.24, 2.76, and 2.97 times, and by 2.43, 1.24, 1.32, and 2.09 times against Candida albicans, Zygosaccharomyces rouxii, Aspergillus niger, and Penicillium roqueforti by the addition of cinnamon EO and clove EO, respectively. Furthermore, the peroxide values were reduced by 16.88% and 15.58% with the addition of cinnamon EO and clove EO. These results indicated that C. reticulata oil nanocapsules' properties could be improved by adding cinnamon EO and clove EO to enhance the use of CEO.