The Maotang site in the northeastern Nanyang Basin, central China, encompasses both the Qujialing (5300–4500 BP) and Shijiahe (4500–4200 BP) cultures. Based on the flotation of soil samples collected at the site, micromorphological identification confirmed the presence of three crop seeds, rice (Oryza sativa), foxtail millet (Setaria italica) and broomcorn millet (Panicum miliaceum), as well as 18 types of non–crop seeds, along with some fruits and nuts. The analysis indicated that during the Qujialing–Shijiahe Cultural period, the Maotang site functioned as a agricultural settlement cultivating a combination of rice and millet. Within this mixed farming, rice and foxtail millet dominated, while broomcorn millet occupied a relatively lower position. Notably, during the Qujialing Culture period, rice had greater significance than foxtail millet, and after entering the Shijiahe Culture period, rice and foxtail millet became nearly equally important. Based on relevant studies on paleoenvironment, agricultural history and archaeological culture, this article argues that cultural diffusion has had a significant impact on the evolution of crop structure during the Neolithic Nanyang Basin. Specifically, the northward expansion of the Qujialing Culture notably established a predominance of rice in the mixed cultivation system, which was more prevalent in the southwestern area of the basin. However, during the Shijiahe Culture period, due to the decline of the Shijiahe Culture's influence and the flourishing of archaeological cultures from the Central Plain, the position of foxtail millet increased obviously, and it nearly had the equal importance as rice in the northeastern area of the Nanyang basin. This study provides the latest archaeobotanical data from the transitional area of the central China, contributing to a further exploration on the relationship between the crop structure evolution and archaeological culture diffusion in the Neolithic period.