Net primary productivity (NPP) is a key vegetation parameter and ecological indicator for tracking natural environmental change. High-quality Moderate Resolution Imaging Spectroradiometer Net primary productivity (MODIS-NPP) products are critical for assuring the scientific rigor of NPP analyses. However, obtaining high-quality MODIS-NPP products consistently is challenged by factors such as cloud contamination, heavy aerosol pollution, and atmospheric variability. This paper proposes a method combining the discrete wavelet transform (DWT) with an extended Kalman filter (EKF) for generating high-quality MODIS-NPP data. In this method, the DWT is used to remove noise in the original MODIS-NPP data, and the EKF is applied to the de-noised images. The de-noised images are modeled as a triply modulated cosine function that predicts the NPP data values when excessive cloudiness is present. This study was conducted in South China. By comparing measured NPP data to original MODIS-NPP and NPP estimates derived from combining the DWT and EKF, we found that the accuracy of the NPP estimates was significantly improved. The MODIS-NPP estimates had a mean relative error (RE) of 13.96% and relative root mean square error (rRMSE) of 15.67%, while the original MODIS-NPP had a mean RE of 23.58% and an rRMSE of 24.98%. The method combining DWT and EKF provides a feasible approach for generating new, high-quality NPP data in the absence of high-quality original MODIS-NPP data.