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Being recognized among the cradles of human civilization, ancient China nurtured the longest continuous academic traditions and humanistic spirits, which continue to impact today’s society. With an unprecedented large-scale corpus spanning 3000 years, this paper presents a quantitative analysis of cultural evolution in ancient China. Millions of intertextual associations are identified and modelled with a hierarchical framework via deep neural network and graph computation, thus allowing us to answer three progressive questions quantitatively: (1) What is the interaction between individual scholars and philosophical schools? (2) What are the vicissitudes of schools in ancient Chinese history? (3) How did ancient China develop a cross-cultural exchange with an externally introduced religion such as Buddhism? The results suggest that the proposed hierarchical framework for intertextuality modelling can provide sound suggestions for large-scale quantitative studies of ancient literature. An online platform is developed for custom data analysis within this corpus, which encourages researchers and enthusiasts to gain insight into this work. This interdisciplinary study inspires the re-understanding of ancient Chinese culture from a digital humanities perspective and prompts the collaboration between humanities and computer science.