Provided are a flight simulation and control method of a unmanned aerial vehicle with regenerative fuel cells and solar cells for high altitude long endurance, and a control apparatus thereof. The high altitude long endurance simulation method for an unmanned aerial vehicle based on regenerative fuel cells and solar cells includes: a variable inputting step of inputting design variables of the unmanned aerial vehicle based on regenerative fuel cells and solar cells; a modeling step of performing modeling of the unmanned aerial vehicle based on regenerative fuel cells and solar cells using the design variables input in the variable inputting step; and an analyzing step of analyzing a modeling result in the modeling step to perform a high altitude long endurance simulation while controlling any one of the design variables input in the variable inputting step.