A method for preparing a molybdenum layer of a copper indium gallium selenium (CIGS) flexible film battery includes the steps of selecting a high-quality polyimide film as a substrate of a CIGS solar cell, cleaning the surface of the polyimide film through a chemical water-bath method, and using a multi-target sputtering method including sputtering at least one sparse molybdenum layer on the positive side of the polyimide film, sputtering at least one dense molybdenum layer on the sparse molybdenum layer, sputtering one coating on the back side to balance the stress of the molybdenum layer on the positive side in the same way. The multi-target sputtering uses at least three sputtering target machines, wherein a first sputtering target machine sputters at least one sparse molybdenum layer on the positive side of a polyimide film, a second sputtering target machine sputters one molybdenum layer on the back side of the polyimide film, and a third sputtering target machine sputters at least one dense molybdenum layer on the sparse molybdenum layer on the positive side. The method is simple and reliable, and can prevent curling of the polyimide film substrate, and prevent falling and curling of a CIGS flexible film solar cell.