The grain production prediction is one of the most important links in precision agriculture. In the process of grain production prediction, mechanical noise caused by the factors of difference in field topography and mechanical vibration will be mixed in the original signal, which undoubtedly will affect the prediction accuracy. Therefore, in order to reduce the influence of vibration noise on the prediction accuracy, an adaptive Ensemble Empirical Mode Decomposition (EEMD) threshold filtering algorithm was applied to the original signal in this paper: the output signal was decomposed into a finite number of Intrinsic Mode Functions (IMF) from high frequency to low frequency by using the Empirical Mode Decomposition (EMD) algorithm which could effectively restrain the mode mixing phenomenon; then the demarcation point of high and low frequency IMF components were determined by Continuous Mean Square Error criterion (CMSE), the high frequency IMF components were denoised by wavelet threshold algorithm, and finally the signal was reconstructed. The algorithm was an improved algorithm based on the commonly used wavelet threshold. The two algorithms were used to denoise the original production signal respectively, the adaptive EEMD threshold filtering algorithm had significant advantages in three denoising performance indexes of signal denoising ratio, root mean square error and smoothness. The five field verification tests showed that the average error of field experiment was 1.994% and the maximum relative error was less than 3%. According to the test results, the relative error of the predicted yield per hectare was 2.97%, which was relative to the actual yield. The test results showed that the algorithm could effectively resist noise and improve the accuracy of prediction.