Abstract: Based on a systematic perspective comprised of economic, “spiritual”, and institutional constraints, a supply chain influencing factor system is proposed. Then, a theoretically hypothesized model of factors is built via the Structural Equation Model method. By following the evolution of partnership, differences of all factors of three aspects are compared and the law of differences is further explored. It shows that profit allocation has always exerted a significant positive impact on incentive mechanism building. The influence is weakening with the evolution of partnership, and special investment plays an increasingly significant positive role in growth and maturity phases. The positive impact of spiritual factors increases, trust is the major positive factor in maturity. Institutional factors have significant impact on mechanism building only in growth phase. These results provide important basis for scientific incentive mechanism building and dynamic adjustment of supply chain.