Grasping the dynamics of carbon emission in time plays a key role in formulating carbon emission reduction policies. In order to provide more accurate carbon emission prediction results for planners, a novel short-term carbon emission prediction model is proposed. In this paper, the secondary decomposition technology combining ensemble empirical mode decomposition (EEMD) and variational mode decomposition (VMD) is used to process the original data, and the partial autocorrelation function (PACF) is applied to select the optimal model input. Then, the long short-term memory network (LSTM) is chosen for prediction. The secondary decomposition algorithm is innovatively introduced into the field of carbon emission prediction, and the empirical results illustrate that the secondary decomposition technology can further improve the prediction accuracy. Combined with the secondary decomposition, the
R
2
, MAPE, and RMSE of the model are improved by 2.20%, 43.08%, and 36.92% on average. And the proposed model shows excellent prediction accuracy (
R
2
= 0.9983, MAPE = 0.0031, RMSE = 118.1610) compared with other 12 comparison models. Therefore, this model not only has potential value in the formulation of carbon emission reduction plans, but also provides a valuable reference for future carbon emission forecasting research.