The present invention provides a method to prevent short of contact and metal lines. The method is applied in a substrate formed with a number of contact windows. The method is comprised of: (a) forming a first conductive layer in the contact windows without filling up the contact windows; (b) forming liners in the contact windows to reduce the openings of the contact windows; (c) forming liner trenches in the contact windows; and (d) forming a second conduction layer on top of the first conductive layer in the contact windows. According to this invention, shorts between contact windows and metal lines is effectively prevented. Therefore, the product yield is greatly improved.