A method of manufacture of an integrated circuit packaging system includes: applying a conductive material on a support structure; providing a bottom integrated circuit package having a bottom lead extended therefrom; attaching the bottom lead to the conductive material; stacking a top integrated circuit package over the bottom integrated circuit package, the top integrated circuit package having a top lead extending therefrom and the top lead over the bottom lead; attaching a conductive paste at an end portion of the top lead; and forming a stacking joint by flowing the conductive paste and the conductive material, the stacking joint below the top lead as well as below and above the bottom lead.