This paper aims to study the application of hyperspectral technology in the classification of deep-sea manganese nodules. Considering the spectral spatial variation of hyperspectral images, the difficulty of label acquisition, and the inability to guarantee stable illumination in deep-sea environments. This paper proposes a local binary pattern manifold superpixel-based fuzzy clustering method (LMSLIC-FCM). Firstly, we introduce a uniform local binary pattern (ULBP) to design a superpixel algorithm (LMSLIC) that is insensitive to illumination and has texture perception. Secondly, the weighted feature and the mean feature are fused as the representative features of superpixels. Finally, it is fused with fuzzy clustering method (FCM) to obtain a superpixel-based clustering algorithm LMSLIC-FCM. To verify the feasibility of LMSLIC-FCM on deep-sea manganese nodule data, the experiments were conducted on three different types of manganese nodule data. The average identification rate of LMSLIC-FCM reached 83.8%, and the average true positive rate reached 93.3%, which was preferable to the previous algorithms. Therefore, LMSLIC-FCM is effective in the classification of manganese nodules.