Abstract: Rock heterogeneity (such as mineral inclusions, micro-cracks, micro-voids and other microstructures) significantly affects its nonlinear mechanical behavior and failure process. This paper utilizes the Fast Fourier transform-based(FFT) numerical method which does not require meshing of complex microstructure but directly obtains the microstructure of heterogeneous materials through the pixels of the image. In addition, the method can be naturally combined with digital image processing (DIP). An actual-microstructure-based FFT method is thereby developed to simulate the elastoplastic behavior of the heterogeneous rocks under external load. The influence of microstructure on the nonlinear behavior is discussed as well as the internal relationship between the microstructure and the macroscopic mechanical properties. The results show that the real-microstructure-based FFT method can well predict the nonlinear behavior before and after the peak strength of the rocks under different depths and confining pressures. The shape, size and distribution of microstructure directly determine the distribution of stress field in clay rock. The actual-microstructure-based FFT method proposed in this paper can reasonably consider the rock heterogeneity, and provides an important tool for studying the influence of the rock microstructure characteristics on the nonlinear mechanical behavior.