This paper presents a segmental autoencoder-based fault detection (FD) framework for nonlinear dynamic systems. The basic idea behind the proposed FD scheme is to identify a generalized kernel representation based on the representation knowledge learned from an autoencoder. By using the system data, several cascades, linking nonlinear operators, are employed to obtain a data-based model which describes the nonlinear dynamic behaviors. With the help of the segmental structure of an autoencoder, a residual generator is then constructed. Rigorous mathematical analysis and an application on a continuous stirred tank reactor demonstrate the effectiveness of the proposed FD method.