Based on relational exchange theory and transaction cost theory, a conceptual model for the relationships among supply chain partnership, inter-organizational knowledge trading and enterprise innovation performance is proposed and empirically tested using the data collected from 256 Chinese manufacturing enterprises in project-based supply chain with the structural equation model. The dimension of supply chain partnership in this model is described from shared goal, trust and relationship commitment. Inter-organizational knowledge trading is categorized into explicit knowledge trading and tacit knowledge trading. The results showed that: (1) there are significant and positive effects of shared goal and trust on explicit knowledge trading, tacit knowledge trading and enterprise innovation performance, while trust has a stronger positive effect on tacit knowledge trading than explicit knowledge trading; (2) although relationship commitment has significant and positive effects on tacit knowledge trading and enterprise innovation performance, it does not affect explicit knowledge trading significantly; (3) it is also proved that inter-organizational knowledge trading (explicit knowledge trading and tacit knowledge trading) has significant and positive effects on enterprise innovation performance; (4) the mediating effects of inter-organizational knowledge trading (explicit knowledge trading and tacit knowledge trading) are proved on the relationships between supply chain partnership (shared goal, trust and relationship commitment) and enterprise innovation performance, excluding the mediating effect of explicit knowledge trading between relationship commitment and enterprise innovation performance. The findings provide a theoretical basis for inter-organizational knowledge trading participants selecting an appropriate relational mechanism to promote knowledge trading, and these also guide the inter-organizational knowledge trading among members of project-based supply chain in practice.