Rice fungal diseases mainly rely on fungal spores for airborne transmission. However, the morphology of various rice disease spores is similar, and it is difficult to distinguish them by traditional spore trap and microscopic image methods. To be able to accurately identify target disease spores and locate the disease source, a multispectral diffraction identification and disease source localization method for rice disease spores was proposed. A large field-of-view, lens-free multispectral diffraction imaging sensor was designed to address the shortcomings of traditional diffraction methods that cannot identify morphological similarities. By analyzing the disease spore diffraction fingerprinting, the multi-spectral diffraction imaging characteristic pattern of rice blast and rice curd spores was analyzed. By integrating the morphological characteristics and absorption properties of spores, two characteristic parameters of fingerprint separation intensity and relative peak difference were proposed to establish the multispectral diffraction identification model of spores. The spore propagation law was analyzed by simulation and calculation experiments, and the diffusion model in the process of spore propagation was established by coupling environmental information. The spatial distribution of spores was analyzed under the conditions of non-directional wind and directional wind, and an iterative plasmodial localization algorithm of the disease outbreak source was proposed. The experimental results showed that the recognition rate of rice disease spores reached 98.5%, and the localization error was as low as 4.9% for undirected wind conditions and 7.1% for directed wind conditions. This method can provide a reference in locating the source of crop disease outbreaks.