Phalaenopsis is one of the most important ornamental crops and is frequently transported between continents. In this study, the effects of the duration and temperature of simulated dark shipping (SDS) and the temperature difference between cultivation greenhouses and shipping containers on the carbohydrate status and post-shipping performance were investigated. With a prolonged SDS from 0 to 40 days at 20 °C, the percentage of the vegetative Phalaenopsis Sogo Yukidian ‘V3’ plants with yellowed leaves increased from 0% to 50%, and the total carbohydrate contents in the shoot and roots gradually decreased over time. Furthermore, roots had greater reductions in glucose and fructose concentrations than the shoot after 40 days of SDS. After 7 days of SDS, the youngest bud and the nearly open bud on blooming plants of Phalaenopsis amabilis were found to be the most negatively affected among flowers and buds of all stages. These buds had lower soluble sugar concentrations and flower longevities compared with those of unshipped plants. The results of a temperature experiment showed that yellowing of the leaves and chilling injury (CI) occurred in Phalaenopsis Sogo Yukidian ‘V3’ after 21 days of SDS at 25 and 15 °C, respectively, regardless of pre-shipping temperature acclimation. However, 10 days of acclimation at 25/20 °C (day/night) before SDS reduced CI and reduced the time to inflorescence emergence. Higher accumulations of sucrose in the shoot and glucose and fructose in roots were found after 21 days of SDS at 15 °C compared with those at 25 and 20 °C. In conclusion, the carbohydrate status of Phalaenopsis was positively related to the post-performance quality. A reduction in the commercial quality after SDS may be attributed to a decline in carbohydrates. The optimal temperature for long-term dark shipping is 20 °C, and we recommend providing 10 days of lower-temperature acclimation (25/20 °C) before shipping to enhance the chilling tolerance and to promote early spiking of Phalaenopsis plants.