The invention relates to a hyperspectral image based overripe Lonicera edulis fruit identification method. The method comprises the following steps: 1, acquiring a hyperspectral image of a Lonicera edulis fruit; 2, sampling fruit and background pixels in the hyperspectral image, analyzing and providing an image background removal function model; 3, removing the image background according to the functional model established in step 2; 4, adopting a median filtering, morphological filtering, spatial processing and threshold determining method to remove noises and determine the position of the fruit; 5, sampling pixels of an overripe fruit and a ripe fruit, selecting a most discriminative waveband through a stepwise forward variable selection method, and adopting a linear discriminant analysis method to establish and discriminate the function models of the overripe fruit pixel and the ripe fruit pixel; 6, classifying all fruit pixels according to the discrimination models established in step 5, and respectively marking; and 7, adopting a majority principle to classify all the fruits. The identification method utilizes the spectral information of objectives and also utilizes the spatial information of fruits, so the discrimination rate is improved.