Mature Dictyophora indusiata fruiting bodies are brittle and broken easily during storage. Peach-shaped Dictyophora indusiata before maturity respond well to refrigerated maintenance, but some cannot resume their development after storage. This study analyzed the effects of refrigerated storage and transportation on the restarted development of Dictyophora indusiata fruiting bodies using quantitative transcriptome analysis. The refrigerated (4 °C, 3 d) peach-shaped Dictyophora indusiata (CK) was used as the control. After induction treatment for 3 d (26 ± 2 °C, 95 ± 3% RH), 81.25% of CK could achieve restarted development and mature (D-M), whereas 18.75% failed (D-P) to restart. Quantitative transcriptome analysis revealed that 1389 and 4451 differentially expressed genes (DEGs) were identified in the D-P and D-M groups when compared with the results for the CK group, respectively. DEG annotation and functional analysis revealed that D-P did not initiate energy and nutrient metabolism. Most DEGs involving the phosphatidylinositol signaling pathway and the MAPK signaling pathway were significantly downregulated or unchanged in the D-P and significantly upregulated in the D-M groups. These results suggested that the phosphatidylinositol signaling pathway may play a crucial role in transmitting environmental signals and initiating the morphogenesis of CK, and that the downstream MAPK signaling pathway may be responsible for signal transmission, thereby regulating cellular activities. This study provides a theoretical basis for regulating the growth and development of postharvest Dictyophora indusiata fruiting bodies.