The invention discloses a cross-subject EEG cognitive state recognition method based on a prototype clustering domain adaptation algorithm. According to the method, the concept of category domains isintroduced, on one hand, on the basis of multi-source domain alignment of labels, feature distribution differences between different categories are considered, structural fine-grained alignment underthe category conditions between different source domains in a feature space is researched, and the problem of category imbalance in the multi-source domains is converted into a mode of the category domains; and prototype theoretical clustering alignment between the source domain and the target domain is carried out, i.e., clustering between similar source domains is carried out on the target domain by taking a dynamic adjustment prototype center as a constraint, and similar features and sparse heterogeneous features between the domains are realized, wherein the former realizes intra-domain class conditional structure feature alignment, and the latter realizes global fine-grained structure feature alignment. According to the invention, the method can be compatible with category balance andimbalance, effectively solves the problem of individual difference of electroencephalogram signals in the field of brain cognitive calculation, has high generalization ability, and can be well suitable for clinical diagnosis and practical application.