A method for filling multi-layer chip-stacked gaps is revealed, primarily comprising the steps as below. Firstly, a chip-stacked assembly is provided, comprising a substrate and a plurality of chips vertically stacked on the substrate where at least a first underfilling gap is formed between each two adjacent ones of the stacked chips with a height difference from the substrate. Then, the chip-stacked assembly is flipped and dipped into an underfilling material where the underfilling material is disposed in a storage tank in a flowing state to completely fill the first underfilling gap. Then, the chip-stacked assembly is taken out. Finally, the chip-stacked assembly is heated to cure the underfilling material filled in the first underfilling gap. Accordingly, multi-layer chip-stacked gaps with different heights can be simultaneously filled at one single step. The conventional underfilling difficulty of multi-layer chip-stacked gaps can be solved leading to higher productivity.