Food and medicine homology resources are increasingly constrained by climate-driven production instability, chemical-residue control, postharvest deterioration, and the demand for function-oriented products. Low-temperature plasma (LTP), also referred to in the literature as cold plasma or non-thermal plasma, is a non-equilibrium physical technology that generates reactive oxygen species (ROS), reactive nitrogen species (RNS), charged particles, electric fields, and ultraviolet (UV) photons under ambient or near-ambient bulk-temperature conditions. This review establishes an end-to-end LTP application framework for plant-, animal-, and microbial-derived food and medicine homology resources. Different from single-sector reviews, the present framework distinguishes substrate-specific regulatory logic across the whole value chain. In plant-derived resources, LTP mainly acts through physical signal-mediated stress priming, secondary metabolism regulation, microbiome modulation, postharvest quality maintenance, detoxification, sensory improvement, and waste valorization. In animal-derived resources, its application logic is centered on environmental biosecurity, feed molecular modification, protein and heme chemistry, and low-loss preservation. In microbial-derived resources, LTP is closely associated with mutagenesis breeding, cell-wall remodeling, community selection, metabolic reprogramming, and biomanufacturing efficiency. The main bottlenecks remain the absence of standardized parameter databases, incomplete understanding of plasma-biomolecule interactions, insufficient scale-up of continuous equipment, and inadequate safety evaluation systems for food and traditional medicinal materials. Future research should prioritize substrate-specific parameter standardization, multi-omics-based mechanistic elucidation, and integration with smart agriculture, precision nutrition, circular economy, and AI-assisted process control. Overall, LTP should be regarded not only as a sterilization or preservation tool, but also as a programmable physical-regulatory platform for full-chain quality formation and high-value utilization of food and medicine homology resources.