Provided is an operation method of a heat engine device using a single ion configured to greatly improve the efficiency of a heat engine by performing work in a different way than heat engine apparatuses to which classical thermodynamics applies. With the single ion heat engine device, a heat engine cycle in accordance with an auto engine cycle can be established on a micro-scale. Accordingly, the heat engine device using single ion has the effect of being able to be utilized as a substantially mesoscopic or nano-scale heat engine. This utilization is based on concepts, such as temperature, entropy, and pressure, that vary with features of a micro-miniaturized heat engine and types of thermal reservoirs and on interpretation of a change in engine efficiency.