The invention relates to a machining technology, in particular to a method for machining a large-depth-diameter-ratio small hole of the glass fiber composite-aluminum alloy layered material. The technology comprises specific steps that firstly, two drill bots of specification sizes are prepared, wherein the drill bits comprise a hard alloy drill bit used for glass fiber composite machining and a high-speed steel drill bit used for aluminum alloy machining; secondly, the thickness of the glass fiber composite layer is measured and recorded, and the thickness of a rubber layer is measured and recorded; thirdly, a product is clamped, and it is ensured that during subsequent machining, tool feeding is achieved from one side of non metal; fourthly, the hard alloy drill bit is clamped, reasonable machining parameters are set, and after the glass fiber composite is subject to peck drilling and is drilled through, tool retreating is achieved; fifthly, the feeding speed is reduced, and peck drilling is carried out until a certain depth is achieved, and tool retreating is achieved; sixthly, the high-speed steel drill bit is replaced, the reasonable machining parameters are set, and peck drilling is carried out until the design depth is achieved, and tool retreating is carried out. Through the method, the problem of the high drill bit breakage rate in the small hole machining can be effectively solved, and the yield is greatly improved.