The invention relates to a manufacturing method of a high-capacity silicon capacitor with a trench structure, and belongs to the technical field of the capacitor. The main technical scheme is performed by the following steps of forming the trench structure; repairing the rough surface of the trench structure; forming a trench insulating layer; performing lamination of an electrode layer and a dielectric layer; etching the electrode layer and the dielectric layer; forming a protection layer and a connecting channel; and forming an external terminal. The electrode layer and the dielectric layer are formed by adopting the continuous lamination method, and next, continuous etching is performed, so that lamination etching damage can be prevented; by adoption of the cross-shaped trench structure, falling off a silicon column can be prevented; and in addition, the silicon capacitor formed by the method only needs one-time via hole operation, so that the operation cost is lowered.