Cordyceps militaris is a well-known edible medicinal fungus. It has a distinctive sensory quality and contains unique nutrients. It undergoes continuous quality degradation, presenting discoloration, moisture loss, texture changes, and nutrient and flavor loss. In this study, fumigation was performed with different concentrations of 1-methylcyclopropene (1-MCP) to study the changes in the postharvest quality and physiological indexes of C. militaris during storage at 4 °C in polypropylene packaging. The results reveal that fumigation with 1.0 μL/L 1-MCP had the best preservation effect. When stored for 24 days, the respiratory intensity was 435.59 mg/(kg∙h), the lowest weight loss rate was 6.62%, the highest hardness was 3.20 N, and the color change was the smallest. The synthesis of cordycepin, polysaccharides, total phenols, and flavonoids was also promoted. Storage inhibited the synthesis of malondialdehyde and the decrease of the peroxidase (POD), catalase (CAT), and superoxide dismutase (SOD) activity, effectively extending the shelf life. This study provides a theoretical basis for the storage and preservation of C. militaris.