The effect of magnetic field (MF) on the postharvest quality and energy metabolism of green chili was investigated. An MF of 4 mT intensity was applied during the refrigeration of green chili pepper. Conventional refrigeration (CR) was used as a control, and the chili pepper fruit was stored at 10 °C and sampled at 1, 5, 10, 20, and 30 d after harvest. The results showed that MF inhibited the senescence of chili pepper and quality deterioration, as evidenced by higher water content, vitamin C (VC) and flesh firmness as well as lower weight loss and decay incidence. The decrease of hue angle values and the chlorophyll content were remarkably depressed by MF treatment, indicating an efficient delay in the yellowing of chili pepper. In terms of metabolism, MF sustained high adenosine triphosphate (ATP) content, energy charge (EC), and activities of key enzymes engaged in energy metabolism (H+-ATPase, Ca2+-ATPase, succinate dehydrogenase, and cytochrome C oxidase). Additionally, there was an increase in the concentration of major energy metabolites, including citric-acid, isocitric-acid, D-Glucose-6-phosphate, and D-Fructose-6-phosphate. These results suggested that MF may be used as a promising strategy for preventing the decay of postharvest green chilies and prolonging their shelf life.