Supply chain system (SCS) is a network control system integrated with a series of facilities that procure raw materials, process them into intermediate goods and the final products, which are distributively delivered to customers. It is an important task to guarantee the stability when the system is suffering external attacks and interference signals, which leads to the system status change accordingly. This paper aims to study the security of the supply chain system with attack and external interference signals. In order to guarantee the stability of the system, zero-sum game framework is constructed, in which the system defense control signal, external attack signal and external interference signal are regarded as participants in the game. The performance index function is constructed through the Hamiltonian function, and the conditional generative countermeasure network fitting is introduced to solve the control gain. And then the optimal control signal is further obtained. Finally, a simulation example verifies that the control signal designed by this method can make the supply chain system reach stability. Finally, a simulation example verifies that the control signal designed by this method can make the SCS reach stability subject to change design.