The oceanic tropospheric duct is a structure with an abnormal atmospheric refractive index. This structure severely affects the remote sensing detection capability of electromagnetic systems designed for an environment with normal atmospheric refraction. The propagation loss of electromagnetic waves in the oceanic duct is an important concept in oceanic duct research. Owing to the long-term stability and short-term irregular changes in marine environmental parameters, the propagation loss in oceanic ducts has nonstationary and multiscale time characteristics. In this paper, we propose a multiscale decomposition prediction method for predicting the propagation loss in oceanic tropospheric ducts. The prediction performance was verified by simulating propagation loss data with noise. Using different evaluation criteria, the experimental results indicated that the proposed method outperforms six other comparison methods. Under noisy conditions, ensemble empirical mode decomposition effectively disassembles the original propagation loss into a limited number of stable sequences with different scale characteristics. Accordingly, predictive modeling was conducted based on multiscale propagation loss characteristic sequences. Finally, we reconstructed the predicted result to obtain the predicted value of the propagation loss in the oceanic duct. Additionally, a genetic algorithm was used to improve the generalization ability of the proposed method while avoiding the nonlinear predictor from falling into a local optimum.