The research on supply chain partnership is one of important areas of supply chain. The relationship between partners has a great impact on the success of supply chain. This paper analyzes many factors influencing the relationship quality of supply chain partners, applies the fuzzy comprehensive evaluation to the relationship quality based on fuzzy mathematics theory, combines the empirical data to evaluate the relationship level of supply chain partners, establishes the factor sets, the evaluation sets and the weight sets, and makes the evaluation of the weight sets by AHP to avoid the effect of individual subjective judgment and favoritism on the result of relationship quality evaluation of supply chain partners. This paper attempts to provide a qualitative and quantitative analysis for studying the relationship quality of supply chain partners, and the results show that the method of fuzzy comprehensive evaluation can be used widely in the researches on supply chain partners.