The fungal inhibitory and preservative effects of essential oils (EOs) on the dominant spoilage fungi of blue honeysuckle were investigated. First, the dominant spoilage fungi (CW1, CW3, and W53) were isolated from naturally infected blue honeysuckle and identified through morphological features, inoculation study, and rDNA-ITS analysis were matched to Alternaria alternata, Metuloidea reniformis, and Rhizopus microsporus, respectively. Next, the filter paper method determined the sensitivity of EOs to the dominant spoilage fungi, and four kinds with better antifungal effects were screened out. Two or three combinations of four EOs were evaluated using a checkerboard analysis method. The fractional inhibitory concentration index (FICI) was used to assess the interactions between the combinations. The combinations of cinnamon/oregano, cinnamon/clove, oregano/clove, and cinnamon/oregano/clove showed synergistic effects (FICI ≤0.5). The best three-oil combination had a volume ratio of 31:8:8 compared to a single oil. Finally, in vivo, experiments showed that combining triple groups of EOs could prevent the spoilage of postharvest honeysuckle. Compared with the control group, the triple groups of essential oil combination maintained the best color, quality, and flavor of blue honeysuckle berries. At the same time, the spoilage rate and the weight loss rate were reduced by 38.50% and 40.71%, respectively. Delayed spoilage time to 3–5 days and the preservation effect of blue honeysuckle was extended to 16 days. Therefore, this study provides a theoretical basis for substituting chemical preservatives and highlights the potential of using complex EOs to prolong the freshness of blue honeysuckle.