During the early and middle periods of the Longshan culture (4600–4200 cal BP), early states developed around the Liangchengzhen and Yaowangcheng sites along the coastal areas of southeastern Shandong. Intensive agriculture and the specialised production of stone tools symbolised the advanced development of Longshan society. However, previous archaeological research in this area has focused mainly on the central settlements of the Longshan culture. As small and medium-sized rural settlements have not been sufficiently explored, their subsistence economy and stone tool functions remain unclear. Starch grains and phytolith assemblages in the residues on stone tool surfaces provide direct tangible evidence of the functions of these tools and offer a new perspective on the characteristics of plant resource use at archaeological sites. The Sujiacun site in Rizhao was a Longshan-period rural settlement in coastal southeastern Shandong. This study conducted starch grain and phytolith analyses of the residues on the surfaces of 17 stone tools from the Sujiacun site. Starch grains of foxtail millet (Setaria italica), broomcorn millet (Panicum miliaceum), rice (Oryza sativa), roots and tubers, and plants of the Hordeum genus were identified, as well as phytoliths of broomcorn millet and rice and those commonly found in grass stems and leaves. This micro-botanical data together with other archaeological evidence suggest that foxtail millet, broomcorn millet, and rice were the main plant foods and that mixed farming of millet and rice was the main subsistence economy at the Sujiacun site. Knives and sickles were mainly used for harvesting crops and sometimes for peeling, slicing, and chopping roots and tubers. The stone muller was used for grinding rather than dehusking grain, and the grinding stone was used not only for polishing stone tools but also for grinding plants. Our findings provide new insights into the methods of plant use and subsistence practices of the Longshan complex society on the east coast of China.