Hongmeiren is a high-quality orange fruit but susceptible to mechanical damage. This work proposes a new packaging format (Packaging C), which used the plastic partition boards to separate the folding plastic basket to avoid the fruits from crushing each other, and used a PU foam layer and placed it along the inside of the EPE foam layer to meet the different sizes of fruits. The results show that under both 3 and 10 h of simulated transportation, Packaging C achieved a much lower damage and decay rates than Packaging A (plastic bulk containers), and this was further verified by the road transportation. Besides, Packaging C could avoid dents in the peel of some large fruits compared to the gift packaging (Packaging B). Although the use of inner packaging could increase the use of packaging, it can reduce the waste of cultivation and transportation resources caused by not being able to deliver the fruit to the consumer, as well as environmental pollution caused by fruit decay. Moreover, low temperature (10 °C) and high humidity (90% RH) during transportation could further reduce the damage and packages at the rear position obtained a higher damage rate than at the front position, but no obvious difference was found between stack heights.