A method to estimate modal frequency based on empirical mode decomposition (EMD) and ensemble empirical mode decomposition (EEMD) is proposed. This method can decrease the difficulties in identifying modal frequency of combine harvesters. First, we used 16 acceleration sensors installed at different test points to collect vibration signals of a corn combine harvester under operating conditions (mass time-varying conditions). Second, we calculated mean value, variance and root mean square (RMS) value of the vibration signals, and analyzed its stationarity of vibration signals. Third, the main frequencies of the 16 points were extracted using the EMD and EEMD methods. Finally, we considered modal frequencies identified by the SSI algorithm as standard, and calculated the fitting degrees of the EMD and EEMD methods. The results show that in different time periods (0~60 s and 60~120 s), the maximum differences of the mean value, variance and RMS value of signals were 0.8633, 171.1629 and 11.3767, and the vibration signal under the operating condition of field harvesting can be regarded as a typical non-stationary random vibration signal. The EMD method had more modal aliasing than EEMD, and when we obtained the fitting equations of EMD, EEMD and SSI methods, the value of the Euler distance between the EMD fitting equation and the SSI fitting equation was 446.7883, while that for EEMD and SSI was 417.2845. The vibration frequencies calculated by the EEMD method is closer to the modal frequencies identified by SSI algorithm. The proposed method provides a reference for modal frequency identification and vibration control in a complex working environment.