Early blight of chili peppers is a common biological disaster that affects the safe production of chili peppers. It is characterized by suddenness and susceptibility and can easily cause significant economic losses. During the growth process of chili peppers, scientific monitoring and early warning of disease infestation during the incubation period is an important prerequisite for ensuring the healthy growth of crops. This paper establishes the spectral characteristics discriminative model of crop disease incubation period using the hyperspectral image with the working band of 400~1 000 nm and the spectral similarity measurement method. Continuous and dynamic monitoring of hyperspectral images of pepper leaves and healthy leaves inoculated with early blight pathogens at different infection stages using a hyperspectral imager.Extract the average spectrum of the region of interest from a series of hyperspectral images collected in the experiment and preprocess it using convolutional smoothing, multivariate scattering correction, and maximum minimum normalization method (SG-MSC-MMN). Then, two measures, spectral angle cosine correlation coefficient, and Chebyshev distance, are proposed as spectral characteristics evaluation parameters for the incubation period of early blight. Finally, principal component analysis (PCA) was used to verify the results of the spectral characteristics discriminative model of the incubation period to realize the visual distribution of the incubation period of samples.The experimental results show that it is feasible to use the spectral angle cosine correlation coefficient and Chebyshev distance as the spectral characteristic evaluation parameters of the incubation period of early blight of pepper and establish the corresponding discriminative model, respectively, and the earliest identifiable time of incubation period of early blight of pepper obtained from these two discriminative models is 24 hours after inoculation.According to the PCA drawing, the spatial distribution of health vaccination samples during inoculation for 24 hours was verified by the two spectral characteristics-based discriminative models for the incubation period proposed in this paper.The discriminative model of the incubation period of early blight of pepper established in this paper can be extended to monitor and identify the incubation period of other crop diseases and provide theoretical reference and method reference for scientific control of the incubation period of crop diseases.