With the advent of the Internet, most firms have shown increasing interest in business-to-business (B2B) electronic commerce as an alternative for gaining competitive advantage in the marketplace. Many existing researchers and practitioners have approached and conducted research on transactions occurring in inter-firm commerce solely through structural conditions, but have failed to reflect the non-structural conditions that commonly arise in B2B electronic commerce. Structural conditions refer to factors that can be negotiated in electronic commerce, such as price, quantity, and shipping period. In contrast, very little research has been conducted on resolving non-structural yet formalized problems in B2B electronic commerce. In particular, the major structural and non-structural conditions that arise in B2B electronic commerce are interconnected in the form of causal relationships. Therefore, to leverage these causal relationships in B2B electronic commerce, this study proposes a B2B electronic commerce negotiation framework based on causal relationship knowledge utilizing Fuzzy Cognitive Maps. Furthermore, a simple prototype was implemented using the proposed method, and its applicability to B2B electronic commerce was demonstrated by applying it to an actual case.