It is well known that the failure mode of complex mechanical equipment are diversified, and the monitoring data for the fault conditions is scarce. Therefore, the research on fault detection of reciprocating plunger pump with fault-free data is significant in theory and application. Due to the lack of prior knowledge of faults, it is always a great challenge for researchers to extract fault features from signals. In this paper, an innovative fault detection method for reciprocating plunger pump is proposed based on unsupervised feature encoder and minimum covariance determination. Firstly, an criterion based on local and global feature mutual information maximization is proposed for unsupervised feature extraction. In addition, an unsupervised training strategy based on negative sampling is proposed to train the encoder, so that the model can converge quickly and improve the stability of model training. Moreover, the fault detection algorithm of reciprocating plunger pump was proposed based on the unsupervised feature encoder and minimum covariance determination. Finally, the effectiveness and superiority of the proposed method are verified by the measured data of reciprocating plunger pump. The results show that the proposed method can accurately detect the faults of reciprocating plunger pump and the detection accuracy is more than 98%. Compared with other methods, the proposed fault detection algorithm has better applicability and accuracy for fault detection with fault-free data.