Integrate imaging technology, spectrum technology and microscope, a novel molecular hyperspectral imaging (MHSI) system based on AOTF (acoustooptic tunable filters) was presented. The system was used to capture hyperspectral images of rat retinal sections selected from three groups: normal(N), diabetic(D), and EPOtreated(E0). By processing hyperspectral images data of 30 samples, single band images and the pseudocolor images of N、D、E0 group are gained. Typical spectra curves of the ONL cells of N、D、E0 are extracted. By analyzing these images, descending order of the ONL thickness is N、E0、D. The experimental results cite that the ONL thickness of E0 group will be increased after EPO treated. By analyzing these spectrums, transmission intensity of D group is generally higher than that of N group in the spectral field from 550 nm to 1000nm and transmission intensity of E0 group is in the middle of D and N. By analyzing spectrum relations, results show the spectral signature of the E0 group was more similar to that of N than that of D to N. The above results suggest EPO may prevent cell apoptosis and has protective effect on rat DR at a certain level. MHSI system may probably provide a potential approach to researching pathogenesis、causes of blindness and drug efficacy of DR in future.