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Accurate and timely fault diagnosis for the diesel engine is crucial to guarantee it works safely and reliably, and reduces the maintenance costs. A novel diagnosis method based on variational mode decomposition (VMD) and kernel-based fuzzy c-means clustering (KFCM) is proposed in this paper. Firstly, the VMD algorithm is optimized to select the most suitable K value adaptively. Then KFCM is employed to classify the feature parameters of intrinsic mode functions (IMFs). Through the comparison of many different parameters, the singular value is selected finally because of the good classification effect. In this paper, the diesel engine fault simulation experiment was carried out to simulate various faults including valve clearance fault, fuel supply fault and common rail pressure fault. Each kind of machine fault varies in different degrees. To prove the effectiveness of VMD-KFCM, the proposed method is compared with empirical mode decomposition (EMD)-KFCM, ensemble empirical mode decomposition (EEMD)-KFCM, VMD-back propagation neural network (BPNN), and VMD-deep belief network (DBN). Results show that VMD-KFCM has advantages in accuracy, simplicity, and efficiency. Therefore, the method proposed in this paper can be used for diesel engine fault diagnosis, and has good application prospects.