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Mustard essential oil (MEO) nanoemulsions fortified with citrus pectin and tween-80 (MEO-NE-PT) or tween-80 (MEO-NE-T) were prepared by high-pressure homogenization followed by ultrasonication, and comparative analysis was performed on the microstructure, storage stability, pH, ionic strength and thermal tolerance between MEO-NE-PT and MEO-NE-T. The application of MEO-NE-PT to the postharvest preservation of ‘Shatangju’ mandarin was evaluated. It was found that MEO-NE-PT exhibited superior stability with smaller fluctuations in particle size and polydispersity index (PDI). The minimum inhibitory concentration (MIC) of MEO-NE-PT was 64 μL/L, much lower than those of MEO (256 μL/L) and MEO-NE-T (128 μL/L). Furthermore, after MEO-NE-PT treatment at 64 μL/L for 6 h, the germination rate of Geotrichum candidum spores was only 6.67%, and the length of the germ tube was only 8.57 μm, both significantly lower than 100% and 165.02 μm for the control group (MEO), respectively. The results of scanning electron microscopy (SEM) revealed that treatment with MEO-NE-PT caused the mycelium of Geotrichum candidum to wrinkle and break apart. Compared with the control group, MEO-NE-PT treatment could significantly reduce the decay rate and quality loss of ‘Shatangju’ mandarin, while delaying the decline in hardness and total soluble solids. As a safe and effective antimicrobial agent, MEO-NE-PT could control the growth of Geotrichum candidum and maintain the post-harvest quality of ‘Shatangju’ mandarin.