Abstract: The hyper-ectral imaging with polarization is an emerging cross-echnology. It has been the key topic to explore the technology in the aerospace, civil and other areas at home and abroad. In particular, imaging spectrometer based on acousto-ptic tunable filter (AOTF) has many advantages compared with the traditional imaging spectrometers both in running mechanisms and in the design of instrument. By studying the principle of AOTF, the working process of AOTF polarization spectral imaging instrument which was used in the experiment was analyzed, the data acquisition system matching with the instrument was made and the system design process based on LabVIEW platform was discussed in detail. At the same time, the LabVIEW program design diagram of each module was given. The function of system was verified through actual scene test. The final result shows that the system can complete the image data collection efficiently and reliably, as well as controlling the hardware of the instrument correctly. In a way, it is of research and practical value for the system.