Nitrogen oxide (NOx) is one of the main pollutants in the regenerated flue gas of Fluid Catalytic Cracking (FCC) unit. Accurate prediction of NOx emission can effectively avoid the occurrence of pollution events in refinery enterprises. Because of the non-stationarity, nonlinearity and long-memory characteristics of pollutant emission data, a new hybrid model incorporating Ensemble Empirical Mode Decomposition (EEMD) and Long Short-Term Memory network (LSTM) was proposed to improve the prediction accuracy of pollutant emission concentration. The NOx emission concentration data was first decomposed into several Intrinsic Mode Functions (IMFs) and a residual by using the EEMD model. According to the correlation analysis between the IMF sub-sequences and the original data, the IMF sub-sequences with low correlation were eliminated, which could effectively reduce the noise in the original data. The IMFs could be divided into high and low frequency sequences, which were respectively trained in the LSTM networks with different depths. The final NOx concentration prediction results were reconstructed by the predicted results of each sub-sequences. Compared with the performance of LSTM in the NOx emission prediction of FCC unit, the Mean Square Error (MSE), Mean Absolute Error (MAE) were reduced by 46.7%, 45.9%,and determination coefficient (R2) of EEMD-LSTM was improved by 43% respectively, which means the proposed model achieves higher prediction accuracy.