The accurate prediction of reference crop evapotranspiration (ET0) is essential to better manage crop irrigation water consumption and improve crop water use efficiency. To effectively improve the accuracy of ET0 simulated by machine learning models, five meteorological stations in Hailaer, Harbin, Hohhot, Changchun, and Dalian were taken as representative stations, daily and monthly ET0 data from 1952 to 2020 were used, and empirical mode decomposition (EMD) and wavelet threshold denoising (WD) were considered. The convolutional neural network (CNN) and long short-term memory network (LSTM) models were improved, and two new hybrid neural network models (EMD–WD–CNN and EMD–WD–LSTM) were constructed. Using the ET0 calculated using the FAO-56 Penman–Monteith (P–M) formula as the standard value, the applicability of the improved machine learning model was evaluated. Results showed the following: i) the daily ET0-PM minimum values of five stations were close to 0, the average values were not significantly increased, and the maximum values significantly fluctuated (the fluctuations in Hailaer and Hohhot showed an upward trend, and the fluctuations in Harbin, Changchun, and Dalian showed a downward trend). The annual average monthly ET0-PM varied seasonally, with the peak in June in the Hailaer station and May in all other stations (the peak in Hohhot was the largest, and the peak in Dalian was the smallest). ii) The daily and monthly ET0 values predicted by the proposed EMD–WD–CNN and EMD–WD–LSTM models were highly consistent with the calculated results of the P–M model, showing high accuracy on the daily and monthly ET0 of the simulated five stations (daily: mean absolute error (MAE), 0.30–0.41 mm/day; root mean square error (RMSE), 0.46–0.60 mm/day; R2, 0.86–0.95; monthly: MAE, 5.66–13.71 mm/month; RMSE, 8.97–18.04 mm/month; R2, 0.91–0.95). iii) The EMD–WD–CNN model was suitable for daily scale ET0 simulation and prediction in Northeast China and monthly scale in Harbin, Changchun, and Hohhot. The EMD–WD–LSTM model was suitable for monthly ET0 simulation and prediction in Hailaer and Dalian in Northeast China. The mixed models of EMD–WD–CNN and EMD–WD–CNN can effectively improve the prediction accuracy of ET0 and can provide a new method for agricultural development and irrigation regulation in Northeast China.