The archaeological sites of Shunshanji and Hanjing are recorded as the earliest Neolithic sites in the middle Huai river valley, China, which were occupied between 8,500 and 7,500 cal bp, and provide crucial evidence of rice growing. However, the water availability and management of arable land systems for rice cultivation and the main stages of rice processing at the two sites have not been studied before. In this paper, phytolith analyses are discussed in 66 samples from the Shunshanji site and 32 samples from the Hanjing site, with three phases of occupation at each. The ratios of sensitive to fixed forms in the phytolith assemblages over three phases reveal that in Phase I these ratios are relatively low, and they become significantly higher in Phases II and III at both sites. These results suggest that rice was grown probably only using natural water supplies in the lowlands during Phase I, but changed to growing on highly controlled and regularly flooded and drained wetlands in Phase II at the two sites. In addition, seen from the distribution and concentrations of phytoliths from rice, weeds and their by-products, as well as the proportions of each, both double peaked glume cells (DPG) and rice cuneiform bulliform cells (RCB) were found together with some rice paddy weed phytoliths. The concentrations of DPG were much higher than those of RCB in most samples from the Shunshanji and Hanjing sites over the three phases. The findings imply that rice ears together with the stems and leaves were probably stored after the harvest, then threshed and de-husked simultaneously, and the straw and chaff by-products were discarded together at the sites between 8,500 and 7,500 cal bp. The study in this paper aims towards a better understanding of past human behaviour and social organization in rice growing communities during the middle Neolithic in eastern China.