At present, there are problems such as low fault data, insufficient labeling information, and poor fault diagnosis in the field of ship engine diagnosis. To address the above problems, this paper proposes a fault diagnosis method based on probabilistic similarity and rank-order similarity of multi-head graph attention neural networks (MPGANN) models. Firstly, the ship engine dataset is used to explore the similarity between the data using the probabilistic similarity of T_SNE and the rank order similarity of Spearman’s correlation coefficient to define the neighbor relationship between the samples, and then the appropriate weights are selected for the early fusion of the two graph structures to fuse the feature information of the two scales. Finally, the graph attention neural networks (GANN) incorporating the multi-head attention mechanism are utilized to complete the fault diagnosis. In this paper, comparative experiments such as graph construction and algorithm performance are carried out based on the simulated ship engine dataset, and the experimental results show that the MPGANN outperforms the comparative methods in terms of accuracy, F1 score, and total elapsed time, with an accuracy rate of 97.58%. The experimental results show that the model proposed in this paper can still fulfill the ship engine fault diagnosis task well under unfavorable conditions such as small samples and insufficient label information, which is of practical significance in the field of intelligent ship cabins and fault diagnosis.