Research in to the nature of Neolithic agriculture in China is often focused on topics such as the domestication and spread of cereal crops and the reconstruction of human and animal diets in the past. Field management practices, such as organic manuring, have not been systematically investigated in Chinese archaeology. Here we present an isotopic dataset for archaeological foxtail millet (Setaria italica) and common millet (Panicum miliaceum) grains as well as associated faunal remains (both domesticated and wild) from seven sites in the Baishui Valley of north China, in order to find direct evidence of organic manuring during the Late Neolithic period. The elevated nitrogen isotope values of the millet grains (5500-3500 cal BP) in comparison with the estimated local vegetation indicates that millets were organically manured by animal dung, mostly likely originating from domestic pigs. Considering the low nitrogen contents of loess soils and their unsuitability for intensive cultivation, this organic manuring by animal dung would have played a key role in maintaining soil productivity and crop yield, which was necessary to support the demands of agriculture and cultural expansion during the Late Neolithic on the Loess Plateau of China.