The invention relates to 5 mu m deep silicon isolation trench forming method, which comprises the following steps of: a, providing a substrate and a masking layer positioned on the substrate; b, coating a photoresist on the masking layer, and forming a masking layer window on the masking layer; c, etching the marking layer at the bottom of the masking layer window; d, removing the photoresist on the marking layer; e, performing plasma etching on the substrate to obtain an isolation trench on the substrate, wherein the depth of the isolation trench is 4.95 to 5.05 mu m; f, cleaning the substrate and the masking layer by using mixed acid solution; g, depositing a spacer medium in the isolation trench of the substrate, wherein the spacer medium is filled in the isolation trench and covers the surface of the masking layer; h, removing the spacer medium on the surface of the marking layer to obtain the spacer medium positioned in the isolation trench; and i, removing the masking layer on the surface of the substrate to obtain the substrate with the isolation trench. The process steps are simple; and the conventional etching apparatus is adopted, the processing cost is reduced, the isolation voltage is improved and the method is stable and reliable.