Scutellaria tsinyunensis C. Y. Wu et Chow is an endangered plant with extremely small populations of endemic species to Chongqing, and we studied the frequency distribution and interspecific association of it and its associated species. We measured the interspecific association between 18 species of herb layer and S. tsinyunensis in nine S. tsinyunensis communities with the help of the 2×2 contingency table, variance analysis, X²Statistics, Ochiai index, Dice and Jaccard index. Combined with the analysis of frequency distribution, we identified the frequency distribution and interspecific association of S. tsinyunensis and its associated species, and discussed the interaction between main herbaceous species in these communities and S. tsinyunensis，which provides a theoretical basis for the protection and utilization of endemic endangered species. The result shows that: (1)the frequency distribution of S. tsinyunensis and its associated species present that: S. tsinyunensis appears to have synergistic effect with Microlepia marginata and Iris japonica, antagonistic effect with Elatostema macintyrei, Lophatherum gracile and Marsdenia tinctoria, while S. tsinyunensis and Dryopteris erythrosora show both synergistic effect and antagonistic effect. (2) The overall correlation dominant species of S. tsinyunensis communities indicate that: six communities present positive correlation, and the other two present negative correlation. (3) Among the 48 species pairs, 34 pairs showed a positive correlation accounted for 70.8% of the total correlation pairs; 14 pairs showed a negative correlation accounted for 29.2% of the total correlation pairs; only 3 pairs showed a significant positive or negative correlation accounted for 6.3% of the total correlation pairs; only 1 pair showed a extremely significant negative connection. It is studied that building environment conducive to the survival of S. tsinyunensis by the way of search for protecting species who are positively correlated with this species, or transplanting them to the communities which distributed positive associated species, is benefit to its population expanding in the wild.