Northwestern China had a pivotal role in the development of a series of Late Neolithic cultures, including the Caiyuan Culture in Ningxia Hui Autonomous Region that spans between 5000 and 4000 BP based on 24 published radiocarbon dates from 9 sites. However, the chronology of the Caiyuan Culture and its relationship to other contemporary cultures in northwestern China remains an ongoing debate, primarily due to the complex cultural attributes between these sites and the conventional 14C dating method. To resolve these issues, 32 bone samples and short-lived charred millet grains from 32 Caiyuan Culture sites have been dated by accelerator mass spectrometry. Based on the material remains, we identified these sites as exclusively belonging to the Caiyuan Culture and applied Bayesian chronological models to refine their chronology to 4450-4000 BP. In comparison with the chronologies and geographic distributions of other Late Neolithic cultures, including Majiayao, Qijia, and Lower Changshan, we argue that the Caiyuan Culture represents an independent trajectory of cultural development in the northwest margin of the Loess Plateau. It was significantly affected by the Banshan Type of the Majiayao Culture and served as an important source of the Qijia Culture, which prevailed widely across the Gan-Qing region and its surroundings during the transition from the Late Neolithic to Early Bronze Age.