In order to improve the accuracy of wheat yellow rust disease severity using remote sensing and to find the optimum inversion model of wheat diseases, the canopy reflectance and disease index (DI) of winter wheat under different severity stripe rust were acquired. The three models of PLS (Partial Least Square), BP neural network using seven hyperspectral vegetation indices which have significant relationship with the occurrence of disease and vegetation index (PRI) were adopted to build a feasible regression model for detecting the disease severity. The results showed that PLS performed much better. The inversion accuracy of PLS method is best than of the VI (PRI, Photochemical Reflectance Index) and BP neural network models. The coefficients of determination (R2) of three methods to estimate disease severity between predicted and measured values are 0.936, 0.918 and 0.767 respectively. Evaluation was made between the estimated DI and the measured DI, indicating that the model based on PLS is suitable for monitoring wheat disease. In addition, to explore the different contributions of diverse types of vegetation index to the models, the paper attempts to use NDVI, GNDVI and MSR which on behalf of vegetation greenness and NDWI and MSI that represents the moisture content to be input variables of PLS model. The results showed that, for the wheat yellow rust disease, changes in chlorophyll content is more sensitive to the disease severity than the changes in water content of the canopy. However, the accuracy of the two models are both lower than predicted when participating in all seven vegetation indices, namely using several species of vegetation indices tends to be more accurate than that using single category. It indicated that it has great potential for evaluating wheat disease severity by using hyper-spectral remote sensing.