This research uses the taboo concept from anthropology to analyze the where the dangerous powers exist indicated by milfoil divination in Zhou Yi, discuss the thinking modes beneath the divination, and trace the development of the thinking modes in later ages. The taboos in Zhou Yi, mostly belong to the presage part under the taboo system, that pre-establish unusual people and things as taboo objects in general, and then reduce risks by putting taboos into practice. The natural taboos in Zhou Yi reflect interactions between heaven and mankind, as well as the unity of all things in the universe; meanwhile, the human taboos in Zhou Yi reflect the interpersonal value of “honesty first.” And the development trends of the taboo thinking in Zhou Yi in later ages include two aspects. First, the taboos in public field tended to disappear, or turned into rites and laws, their mystery faded away, dominated by human demand instead, but the mystery of minor taboos increased and systematized, turned into religions finally. Second, the inner thinking of taboos in private field tends to hold on even though the performance of taboos would differ from age and region, like the sense of uncertainty for personal future, and the worship for the things beyond human power, still last in modern society.