The invention discloses a method for forming high aspect ratio isolation in a high energy ion implantation technology. The method comprises the following steps of S1, preparing a silicon substrate and setting a silicon substrate epitaxial layer, a grinding stopping layer and a masking pattern layer on the silicon substrate in sequence from bottom to top; S2, carrying out high aspect ratio groove etching on the above-mentioned structure, wherein groove bottoms are located on the silicon substrate and are close to the silicon substrate epitaxial layer; S3, selectively and epitaxially growing single-layer or multilayer monocrystalline silicon at the outer side of the above-mentioned structure, wherein the whole grooves are filled up by the monocrystalline silicon; and S4, chemically and mechanically grinding the epitaxially grown monocrystalline silicon in the grooves, stopping in the grinding stopping layer and removing the residual grinding stopping layer. According to the method, the depth limit of the high energy ion implantation technology and the CD or aspect ratio limit of photoetching can be overcome, and the technical problem of driving photodiode pixel units of a CMOS graph sensor product to relatively small sizes and relatively high depth can be solved.