According to the configuration requirement of an InGaAs shortwave infrared detector, a FPGA-based configuration method for the shortwave infrared detector is proposed. Taking a FPGA as a core processor, the configuration of the shortwave infrared detector is implemented in VHDL language. A RS-232 interface is used to communicate with the host computer, to send and adjust the parameters such as the data output order of the detector online and to send the instruction for switching the Integrate Then Read (ITR) and Integrate While Read (IWR) operation modes of the detector. The practical application shows that the configuration method can make the detector operate well and adjust the operation mode and configuration parameters of the detector flexibly. It meets the practical configuration requirements of the shortwave infrared detector.