Line loss prediction of ultrahigh voltage transmission lines is the key for ensuring the safe, reliable, and economical operation of the power system. However, the strong volatility of line loss brings challenges to the prediction of transmission line loss. For more accurate prediction, this article uses ensemble empirical mode decomposition (EEMD) to decompose the line loss and proposes the EEMD–LSTM–SVR prediction model. First of all, this article performs feature engineering on power flow, electric energy, and meteorological data and extracts the exponentially weighted moving average (EWMA) feature from the line loss. After the integration of the time dimension, this article mines the curve characteristics from the time series and constructs a multidimensional input dataset. Then, through ensemble empirical mode decomposition, the line loss is decomposed into high-frequency, low-frequency, and random IMFs. These IMFs and the standardized multidimensional dataset together constitute the final input dataset. In this article, each IMF fusion dataset is sent to LSTM and support vector regression models for training. In the training process, the incremental cross-validation method is used for model evaluation, and the grid search method is used for hyperparameter optimization. After evaluation, the LSTM algorithm predicts high-frequency IMF1 and 2 and random IMF4 and 5; the SVR algorithm predicts low-frequency IMF6 and 7 and random IMF3. Finally, the output value of each model is superimposed to obtain the final line loss prediction value. Also, the comparative predictions were performed using EEMD–LSTM, EEMD–SVR, LSTM, and SVR. Compared with the independent prediction models EEMD–LSTM and EEMD–SVR, the combined EEMD–LSTM–SVR algorithm has a decrease in mean absolute performance error% by 2.2 and 25.37, respectively, which fully demonstrates that the combined model has better prediction effect than the individual models. Compared with that of SVR, the MAPE% of EEMD–SVR decreases by 11.16. Compared with that of LSTM, the MAPE% of EEMD–LSTM is reduced by 32.72. The results show that EEMD decomposition of line loss series can effectively improve the prediction accuracy and reduce the strong volatility of line loss. Compared with that of the other four algorithms, EEMD–LSTM–SVR has the highest R-square of 0.9878. Therefore, the algorithm proposed in this article has the best effectiveness, accuracy, and robustness.