In order to realize the rapid and real-time data pre-processing of an imaging spectrometer based on Acousto-optic Tunable Filter(AOTF), the data characteristics and a pre-processing algorithm of the imaging spectrometer based on AOTF were analyzed. Then, a scheme of dual Digital Signal Processor(DSP) parallel processing system based on two chips of ADSP-TS201 coupled the external bus sharing and the link ports was proposed by using DSP instead of the traditional computer processing platform as the key device. Proceeding from practical requests, a pipeline processing was designed, pre-processing tasks were allocated rationally, and the functional verification was implemented. The practical application shows that it takes 23.5 ms to accomplish the pre-processing task for one frame data of imaging spectrometer based on AOTF, which increases 13 times than that of PC and meets the real-time requirement. The system proposed in this paper promotes the development of systematism, modularization, miniaturization and the capability of real-time processing of the imaging spectrometer based on the AOTF.