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Testing process is essential for instrument both before it can be installed in wafer fabrication equipment and during instrument diagnosis when error happens in equipment. Card configuration system is indispensable for an instrument testing system, for it is used to generate test signal and receive feedback signal from instruments. This paper proposes a flexible card configuration method to meet the need of large-scale instrument testing in wafer fabrication equipment. The method is based on some an established model under constraints of signal-generating cards in instrument testing, and it can support multiple communication types used in wafer fabrication equipment. The concept of virtual channel is proposed to accommodate the system to various communication protocols, and card configuration mode is used to adapt itself to different deployment case. A serialization and deserialization mechanism of card configuration is used to provide instrument testing of both single-time mode and non-continuous mode. The implemented card configuration system is integrated into an instrument testing platform, and it is proved to be both effective and efficient for instrument testing.