Wild Chinese prickly ash with elevated antioxidants is a valuable genetic resource for Zanthoxylum bungeanum Maxim improvement. There are rich wild germplasm resources in the Qinling Mountains. In a study with wild germplasm resources from different altitudes and six cultivated varieties, the phenolic and flavonoid compounds were analyzed by high performance liquid chromatography (HPLC). The chromatograms of them were basically the same, although their chemical composition content was greatly different. The thirty samples were divided into three categories through the hierarchical clustering analysis. And catechin, hyperoside and quercitrin were considered to be key compound for the quality evaluation, by contrast, the wild samples with an altitude of 2300±50 m (Ⅳ group) had the highest content of key compounds, and showed stronger antioxidant activity and antibacterial ability, indicating that these wild samples could be used as an excellent breeding resource. This is the first time to evaluate the quality of wild Chinese prickly ash in different altitude areas of Qinling Mountains. These excellent wild germplasm resources provided substantial potential accessions for use directly in Chinese prickly ash breeding programs.