The skulls were found in two groups at the Shimao Ruins in northwest China's Shaanxi Province.
Majority of the skulls belong to young women, which suggests the outbreak of mass violence or ethnic conflict in the region since ancient people were prone to use their enemies or captives as sacrifices, scientists said.
First two groups of skulls were found in two pits, with 24 skulls in each, in front of the east gate of the city ruin while others were unearthed along the eastern city wall, said Sun Zhouyong, deputy head of the Shaanxi Provincial Institute of Archaeology.
Sun said the skulls will aid research on the religious thinking, construction concepts and cultural activities of people living along the Yellow River Basin over 4,000 years ago.
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The Shimao Ruins were first discovered in 1976 in the shape of a small town, the report said.
Last year, archaeologists identified the ruins as the largest of their kind from neolithic times after measuring the exact size of the ancient stone city.