Cynanchum thesioides (C. thesioides) is a sand-dwelling edible and medicinal plant whose fruit softens rapidly after harvest, limiting its storage life. In this study, we investigated the efficacy and underlying mechanisms of alternating magnetic field (AMF) treatment as a non-thermal and eco-friendly preservation method for C. thesioides fruit. Freshly harvested fruits were subjected to AMF at varying field intensities (1.07–1.54 mT) and exposure durations (5–25 min). We monitored the physiological indicators (respiration rate, membrane permeability, and firmness) during storage to determine the optimal conditions and performed transcriptome sequencing to identify differentially expressed genes, with qRT-PCR validation of two key cell wall-degrading genes (β-glucosidase (BG) and polygalacturonase (PG)). The results showed that AMF treatment at 1.28 mT for 15 min best maintained the postharvest quality, significantly reducing respiration and membrane leakage while delaying firmness loss. Transcriptomic analysis identified 2480 differentially expressed genes enriched in hormone signaling and cell wall metabolism pathways, and qRT-PCR confirmed that AMF downregulated BG and PG expression, suggesting suppressed cell wall degradation and delayed softening. In conclusion, AMF treatment effectively prolonged the shelf life of C. thesioides by modulating the expression of cell wall-related genes. These findings provide novel insight into magnetic field-induced fruit preservation and support AMF as a green non-thermal postharvest technology.