The spectral characterization of flow-field parameters provides a new perspective for understanding the spatiotemporal evolution of unsteady supersonic exhaust plumes and for extracting typical structures. In this study, a large-eddy simulation is performed to calculate the three-dimensional unsteady supersonic plume flow field of rocket engines, and a spectral proper orthogonal decomposition (SPOD) method with a spatiotemporal separation is established. This approach is used to extract the coherent structural features of the unsteady exhaust plume flow field and analyze the mode space structure at different frequencies. The three-dimensional reconstruction and denoising of the exhaust plume flow-field parameters can be achieved via the frequency- and time-domain reconstructions of the SPOD algorithm and oblique projection method, respectively. The ground rocket exhaust plume of ballistic evaluation motor-II is analyzed. The results indicate that the SPOD method can effectively extract the single-frequency mode structure of the reactive supersonic flow field, and that low-order behavior appears in the m = 0 and m = 1 azimuth modes. The potential core exhibits a high-frequency wave-packet structure that is affected by shock waves and shear layers. Time-domain reconstruction based on the oblique projection method facilitates the capture of the dynamic characteristics of the flow field. For the first-order SPOD mode, the frequency- and time-domain reconstruction errors are 3.3% and 1.5%, respectively. The frequency-domain reconstruction method exhibits a 4% improvement in denoising ability compared to low-pass filters. This study provides a novel method for the spectral characterization and spatiotemporal feature extraction of supersonic exhaust plume flow fields.