A method for manufacturing a semiconductor structure including the following steps is provided. First, a first insulating layer with a conductive contact is formed over a substrate, and a second insulating layer having an opening is formed on the first insulating layer, wherein the opening corresponds to and exposes a top surface of the conductive contact. A conductive line structure is formed in the opening, wherein a contact void is formed between the second insulating layer and the conductive line structure, and then a plasma oxide layer is conformally deposited over the substrate. Then, a wet cleaning process is performed by using an aqueous solution containing negatively charged ions. A capping layer is formed on the plasma oxide layer, the capping layer filling the contact void, and an etching back process to remove the capping layer above the contact void.