AbstractDeveloping a method to detect internal leakage in hydraulic cylinder, which is used for Electro‐Hydrostatic Actuators (EHA), is important to prevent serious malfunctions for aircrafts. At present, the internal leakage in an EHA cannot be accurately detected only using operational data. This paper proposed a convolutional neural networks (CNN) based method to detect internal leakage in hydraulic cylinder according to the relationship between operational state parameters of EHA and leakage in the hydraulic cylinder. A method was presented to align multi‐source signals with different forms by using the motor current as a benchmark. Because the number of monitoring signals are relatively small, a feedforward neural network (FFNN) based data augment method is proposed to increase parameters of input data set. A general method on how to detect internal leakage by combining signals alignment, data augmentation and multiscale residual CNN was proposed. The experimental results show that the proposed method can be used to accurately detect internal leakage in a hydraulic cylinder operating under non‐stationary load and velocity conditions, and the detection accuracy reached 99.8%.