A method and system for screening spectral indexes of rice resistant to bacteria. The method includes: processing spectral data of a test sample by a threshold segmentation algorithm to obtain average spectral information of each spectral image and a proportion of lesions corresponding to each spectral image; training a deep learning algorithm model based on a self-attention mechanism by using the average spectral information of each spectral image and the proportion of the corresponding lesions to construct a regression model for evaluating an area of the lesions; determining an optimal band combination and a weight value corresponding to each band in the optimal band combination based on the regression model for evaluating the area of the lesions, and then determining the spectral indexes; and identifying differences between rice of different genotypes at different times of infection by using the spectral indexes, and screening rice varieties resistant to bacterial blight.