Sex-related differences on phenolic profiles, chemical composition of essential oils, anatomy, histochemistry and biological activities (antioxidant and antibacterial activities) of Juniperus rigida needles collected from Yijun and Fugu region were first studied. In two regions, female and male had similar contents of total phenolic and total flavonoid. 10 phenolic compounds were analyzed by RP-HPLC, amentoflavone content was significantly higher in female than male in Yijun, and chlorogenic acid content was significantly higher in female than male in Fugu. 30 compounds (over 0.5 %) were detected in the essential oils, and the total contents of female were lower than male in Yijun. This difference mainly comes from Germacrene D, which was about twice as high in male as in female. Male needles had significantly larger mechanical tissue and phloem in Yijun. Histochemical analysis indicated that the phenols were stored in epidermal cells, sponge tissue, endodermis cells, edge of resin duct, stomatal bands, and the flavonoids were stored in epidermal cells, endodermis cells, edge of resin duct, stomatal bands. No sex-related differences were found in histochemical analysis, antioxidant activities (ABTS, FRAP) and antibacterial activities (9 strains). This preliminary study provided a reference for production practice and theoretical research of J. rigida.