The ancient cultural practice of cranial modification is widely distributed throughout the world. It has a highly symbolic visual feature and is related to various societal aspects such as hierarchy, status, aesthetics and religion. Cranial modification can also be considered a result of infant-rearing behaviors in ancient times. The earliest clue to cranial modification in China came from the Paleolithic, but it was not until the Neolithic that it became a widespread cultural practice later flourishing. Cranial modification in prehistoric China is classified into tabular-annular modification system and occipital modification system. Both originating locally, these two systems have different appearances, distributional ranges, and developmental processes. Tabular-annular modification, originated in northern Northeast China, exhibits prominent cosmetic features and requires complex technology. It is considered to be the earliest known conscious cranial modification practice and may have continued into the historic period. The origin of this tabular-annular modification may be correlated with unique geographic and environmental resources of Northeast China along with a growing complexity of gathering-fishing-hunting society, a gender division of labor, and the hierarchical differentiation existent in a transitional phase from Paleolithic to Neolithic. Occipital modification, centered in the Yellow River basin, is characterized with less pronounced modifications and probably required simpler techniques. It was once widely popular in the late and final Neolithic. Occipital modification may derive from behaviors of infant-rearing in northern agricultural societies and gradually evolved into a conscious cultural practice. Its decline at the end of the Neolithic and eventual disappearance after the Bronze Age was closely connected to societal changes occurring during the Late Neolithic, especially in the Longshan-Erlitou cultures. Both tabular-annular and occipital modification systems vary in skull morphology and measurement data suggesting that modification tools, techniques, and procedures were diverse. Existing studies on cranial modification are dominated by qualitative descriptions, with detailed observation and more systematic measurements necessary for future studies, as well as more refined archaeological contextual information.