In this work, a large eddy simulation (LES) of a typical subsonic diffuser provides data used to analyze coherent structure in a separated flow with dynamic mode decomposition (DMD). From this, a low–dimensional approximation, which retains the main dynamic characteristics of the original flow fields, is obtained. In particular, specific dynamic structures associated with a unique frequency are isolated. The spatial structures of the real and imaginary parts of the DMD mode are similar but with a phase difference. The contribution of the conjugate modes to the evolution of the DMD modes over time is discussed. The dominant frequency is found to be related to the wake mode. The scale of wake will saturate, and the shear layer will become weaker and merges into the wake structure as it develops downstream. This allows direction for effective flow control strategies using this information.