This case study of the early Neolithic Guanjia site (6100–5500 BC) combines zooarchaeological, paleobotanical, and isotope research to investigate how humans raised pigs and incorporated them in their overall subsistence system. Although the teeth (M₂) of Sus scrofa from Guanjia were all larger than domesticated pigs dating to the middle Neolithic (Yangshao period, 5000–3000 BC) and early Bronze Age (2000–1000 BC), which would suggest that Guanjia pigs were not domesticated pigs morphologically if body size is a key criterion to identify domesticated animals, we still argue that there was human management of pigs via feeding and culling strategies. We base our argument on the following observations: (1) Sus scrofa accounts for 34.2% (n = 41) of NISP and 22.2% (n = 4) of MNI; (2) most individuals were younger than two years at time of death (mandible n = 5, epiphyseal fusion n = 14) and most are female; (3) distorted alignment of teeth, a deformation related to early domestication, was found on one left mandible; (4) compared to pure C₃ diets seen in deer (δ¹³C = − 21.0 ± 0.7‰, n = 3), the majority of Sus scrofa consumed some C₄ plants (δ¹³C = − 17.4 ± 0.8‰, n = 6), probably from C₄ wild grass or cultivated millets; (5) Panicoideae starch grain, broomcorn millet (Panicum miliaceum), and foxtail millet (Setaria italica) phytoliths were found at Guanjia, further supporting our argument that Sus scrofa accessed C₄ millets and human environments. This study also reveals that animals in the early stages of domestication and domestic plants only accounted for a small proportion of human subsistence; thus, people still relied heavily on hunting and gathering at Guanjia.