The present invention discloses a method for manufacturing thin film structure, which comprises the following steps: providing a substrate having a first recess and a second recess formed therein with the first recess being deeper than the second recess; depositing a first material layer and a second material layer of different thicknesses successively on the substrate; and grinding the substrate so that a flat upper surface is formed and the first material layer and the second material layer are remained in the first recess while only the first material layer is remained in the second recess. The present invention also discloses a method for manufacturing fringe field switching type liquid crystal display array substrate. With the present invention, it is possible to make the upper surface flat while forming patterns on two layers of thin films respectively by using a single mask.