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As a critical power source, the diesel engine is widely used in various situations. Diesel engine failure may lead to serious property losses and even accidents. Fault detection can improve the safety of diesel engines and reduce economic loss. Surface vibration signal is often used in non-disassembly fault diagnosis because of its convenient measurement and stability. This paper proposed a novel method for engine fault detection based on vibration signals using variational mode decomposition (VMD), K-means, and genetic algorithm. The mode number of VMD dramatically affects the accuracy of extracting signal components. Therefore, a method based on spectral energy distribution is proposed to determine the parameter, and the quadratic penalty term is optimized according to SNR. The results show that the optimized VMD can adaptively extract the vibration signal components of the diesel engine. In the actual fault diagnosis case, it is difficult to obtain the data with labels.