Human settlement and agricultural development are closely linked to local geomorphological and climatic environments. However, the variation in agricultural systems in different environmental and prehistoric contexts remains unknown. We report new archaeobotanical and radiocarbon dates from 34 Neolithic and Bronze Age sites in the Hutuo River Valley (HTRV) in north-central China and compare them with updated archaeobotanical studies in the Sushui River Valley (SSRV) and Henan Province (HNP), to explore the similarities and differences of agricultural patterns under different geomorphologic and climatic environments in north-central China. Our results reveal that humans consistently cultivated foxtail and broomcorn millet in the HTRV from the Miaodigou (6000–5700 cal. a BP) to the Shang-Zhou (3600–2256 cal. a BP) period, despite the introduction of wheat and barley into the area around 4000 a BP. Climate conditions and hilly landforms in the HTRV, SSRV and some parts of the HNP led people to develop foxtail and broomcorn millet dry land farming practices between 7000 and 3000 a BP. Alternatively, in other areas of the HNP, the climate conditions and alluvial plains enabled people to develop a mixed agriculture of millets, soybeans, and rice from 7000 to 4000 a BP, with the addition of wheat between 4000 and 3000 a BP. Farmers’ different agricultural technologies and interactions with foreign cultures may have also influenced the formation of different agricultural patterns in the three regions between 7000 and 3000 a BP. Population growth during 7000–3000 a BP can explain the overall propensity of the higher-yield foxtail millet rather than broomcorn millet as the main cultivated crop. In the HTRV, however, higher proportions of broomcorn millet (as compared to the SSRV and HNP), may reflect the greater drought and heat tolerance of broomcorn millet, representing an adaptive agricultural strategy in the river valley.