Hydraulic systems are a class of typical complex nonlinear systems, which have been widely used in manufacturing, metallurgy, energy, and other industries. Nowadays, the intelligent fault diagnosis problem of hydraulic systems has received increasing attention for it can increase operational safety and reliability, reduce maintenance cost, and improve productivity. However, because of the high nonlinear and strong fault concealment, the fault diagnosis of hydraulic systems is still a challenging task. Besides, the data samples collected from the hydraulic system are always in different sampling rates, and the coupling relationship between the components brings difficulties to accurate data acquisition. To solve the above issues, a deep learning model with multirate data samples is proposed in this article, which can extract features from the multirate sampling data automatically without expertise, thus it is more suitable in the industrial situation. Experiment results demonstrate that the proposed method achieves high diagnostic and fault pattern recognition accuracy even when the imbalance degree of sample data is as large as 1:100. Moreover, the proposed method can increase about 10% diagnosis accuracy when compared with some state-of-the-art methods.