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Capparis trinervia (family Capparaceae) is a common wild plant distributed in various localities in the mountainous region of Vietnam. While essential oils have been found in the leaves and stems of C. trinervia, there are no reports to date describing the chemical composition and biological activities to guide further exploration and application of the oils. This study determined the essential oil composition of C. trinervia; 8 and 23 distinct essential oil compounds were identified from C. trinervia leaves and stems, respectively. Stigmasterol (C29H48O) was identified as the primary compound of essential oil from leaves, accounting for 75.775% of the oils, while 3,7,11,15-tetramethyl-2-hexadecen-1-ol (C20H40O) was identified as the main essential oil component in C. trinervia stems, accounting for 18.337%. This study also explored the cytotoxic effects of essential oils extracted from C. trinervia against five cancer cells lines (A549, MCF7, HeLa, HepG2 and KB). A strong cytotoxic effect on all cancer cell lines was demonstrated by 100 µg mL−1 essential oils derived from C. trinervia leaves and stems, which suggests the species is a promising candidate for use in life and public healthcare.