Located in the transitional region between northern and southern China, the middle Han River valley is of pivotal significance for current debates on rice domestication and the formation of mixed farming in early China. Based on phytoliths and macro-plant remains from 10 sites, along with radiocarbon dating, this study has narrowed the 2000-year gap in early rice utilization by 700 years in the middle Han River valley, and demonstrated the continuous development of rice agriculture in this region. This new evidence also reveals that as early as 7000 cal. BP, mixed farming emerged in this region and facilitated the further southward dispersal of foxtail millet and broomcorn millet into southern China and beyond. In addition, a sample-by-sample comparison of our results with phytoliths and macro-plant remains highlighted the potential biases inherent in these methods. This work emphasized the importance of multi-index archaeobotanical analysis to reconstruct ancient crop assemblages.