This study is subject to 3D virtual simulation and experiment design method application in the optimal clearance design in the 3D shell punched processing. During the simulation stage, the PAM-CRASH and 3D-CAD (Pro/E) system are used to model the punching processing. The results of the punching maximum punched burr from the 3D virtual punching simulation were input to a neural network to establish a model corresponding to the 3D shell punched variables. Once the metal punching control parameters, such as punch/die radius, punch/die clearance, punch cutting angle and different material thickness, were given, the punching processing performance (the punching maximum burr and maximum stress) can be accurately predicted by this developed network. Therefore, in this research, a satisfactory result based on the simulation verification is established.