A method of manufacture of an integrated circuit packaging system includes: providing a package substrate having a component side and a system side; depositing a solder resist layer on the component side of the package substrate; patterning groups of access openings and a die mount opening in the solder resist layer; attaching an integrated circuit die in the die mount opening; forming conductive contacts in the access openings; and attaching system interconnects to the system side of the package substrate including controlling a coplanarity of the system interconnects by the solder resist layer.