[Objective] To clarify the characteristics of innate immune physiological responses induced by chitin and flagellin-derived peptide flg22 in pepper seedlings, and to explore the relationship between innate immune physiological responses and pepper multiple resistance to diseases. [Methods] Five local pepper cultivars from Sichuan were used as experimental materials in this study. The disease indexes of bacterial wilt and phytophthora blight in pepper seedlings were analyzed. Meanwhile seedlings were cultured by hydroponics and treated with chitin and flg22 exogenously. Among different pepper cultivars， under different induction times, seedling root growth, stomata aperture, callose deposition, reactive oxygen species (ROS) accumulation, SOD, CAT activities as well as the changes of related gene expression were checked . Then the physiological responses and theirs relationship with disease resistance were evaluated comprehensively by using biostatistics.[Results] (1) The results showed that the lowest disease index of bacterial wilt and phytophthora blight was 'CT10' cultivar, was the strongest disease resistance, and the highest disease index of bacterial wilt and phytophthora blight was 'TJ' cultivar, was the weakest disease resistance.(2) Exogenous chitin and flg22 inhibited the root growth rate of pepper seedlings in five cultivars, induced stomatal closure on detached leaves, promoted the accumulations of callose deposition in leaf cell wall, increased ROS content constantly with improved SOD and CAT activities continuously. By calculating the average membership function value of the innate immune physiological response index of each different cultivar, it showed that the highest was 'CT10' and the lowest was 'TJ'. The average membership function value has a significant negative correlation with the disease index of bacterial wilt and phytophthora blight .(3) Exogenous flg22 and chitin induced some innate immune involved genes of 'CT10' seedlings significantly upregulation expressions, like CaWRKY22, CaMAPK7 and ChiIV3.[Conclusion] Exogenous flg22 and chitin induced the innate immune physiological responses in pepper seedlings, and the strength of the responses showed different among different varieties. Based on the membership function, the disease resistance level of pepper varieties was evaluated comprehensively. The results showed the average membership function of 'CT10' was the highest and the multi-resistance level was the best, which was related to the significant up-regulated expression of innate immune involved genes CaWRKY22, CaMAPK7 and ChiIV3.