In this paper, with multidimensional urban-rural gaps as undesired outputs, we use the Hicks-Moorsteen index to measure and analyze inclusive total factor productivity (TFP) in provincial level data. Using the dynamic GMM estimation method, we analyze the influencing factors of inclusive TFP index. The results show: First, the inclusive TFP which including multidimensional urban-rural gaps is much smaller than the traditional TFP. The rapid decline in technological progress is an important reason for the decline of the TFP. Second, the inclusive growth is higher in eastern region than those in the central and western regions, and there are regional differences in inclusive economic growth. Third, the urban-rural industrial gap in the lagging phase has a significant negative impact on inclusive economic TFP. There is an “inverted U-shaped” relationship between economic development and inclusive economic TFP in the whole country and the central and western regions while the economic development is positively related to inclusive economic growth in the eastern region where the urban-rural gap is smaller. The urbanization rate contributes to the inclusive economic growth of the whole country and the east and central regions, but is negatively correlated with the inclusive economic growth of the western region. Industrial structure has a suppressive effect on inclusive economic growth. Thus, to promote economic inclusion, it is necessary to narrow the gap between urban and rural industrial development, promote a rational industrial layout, and adopt different development strategies according to the different economic development stages of each region as well as urban and rural development stages.