Implicit large-eddy simulation of an over-expanded screeching rectangular jet is performed with a seventh-order finite difference scheme. Good agreement is found between the predicted flow- and acoustic fields with the experimental observations. Fourier decomposition, phase-averaging analysis and Spectral Proper Orthogonal Decomposition (SPOD) are used to investigate the origin of the screech, the shock leakage during the shear-layer flapping, and the distinguishing fluctuating characteristics in the minor- and major-axis plane of the rectangular jet. It finds that the screech is radiated from the end of the forth shock cell, where the interaction of the shock waves with the shear layer causes periodic leakages of shock-wave tips in the minor-axis plane, resulting in the generation of intense acoustic waves in the surrounding air. An obvious flapping mode at the same frequency of the screech is captured in the minor-axis plane and dominates the dynamic motions of the rectangular jet. The SPOD modes of pressure and velocity fluctuations at the screech frequency help to reveal the relationship between the screech generation and the coherent structures.