An Improved Particle Swarm Optimization Algorithm-Support Vector Regression Machine (IPSO-SVR) prediction model is developed in this paper to predict the electromagnetic (EM) scattering coefficients of the three-dimensional (3D) sea surface for large scenes in real-time. At first, the EM scattering model of the 3D sea surface is established based on the Semi-Deterministic Facet Scattering Model (SDFSM), and the validity of SDFSM is verified by comparing with the measured data. Using the SDFSM, the data set of backscattering coefficients from 3D sea surface is generated for different polarizations as the training samples. Secondly, an improved particle swarm optimization algorithm is proposed by combining the Particle Swarm Optimization (PSO) and Genetic Algorithm (GA). The combined algorithm is utilized to optimize the parameters and train the SVR to build a regression prediction model. In the end, the extrapolated prediction for backscattering coefficients of the 3D sea surface is performed. The Root Mean Square Error (RMSE) of the IPSO-SVR-based prediction model is less than 1.2 dB, and the correlation coefficients are higher than 91%. And the prediction accuracy of the PSO-SVR-based, GA-SVR-based and IPSO-SVR-based prediction models is compared. The average RMSE of the PSO-SVR-based and GA-SVR-based prediction models is 1.4241 dB and 1.6289 dB, respectively. While the average RMSE of the IPSO-SVR-based prediction model is reduced to 1.1006 dB. Besides, the average correlation coefficient of the PSO-SVR-based and GA-SVR-based prediction models is 94.36% and 93.93%, respectively. While the average correlation coefficient of the IPSO-SVR-based prediction model reached 95.12%. It demonstrated that the IPSO-SVR-based prediction model can effectively improve the prediction accuracy compared with the PSO-SVR-based and GA-SVR-based prediction models. Moreover, the simulation time of IPSO-SVR-based prediction model is significantly decreased compared with the SDFSM, and the speedup ratio is greater than 15.0. Therefore, the prediction model in this paper has practical application in the real-time computation of sea surface scattering coefficients in large scenes.