Four lignans, asarinin (1), horsfieldin (2), 5-(4-(3,4,5-trimethoxyphenyl)hexahydrofuro[3,4-c]furan-1-yl)benzo[d][1,3]dioxole (3), 5-(4-(3,5-dimethoxyphenyl)hexahydrofuro[3,4-c]furan-1-yl)benzo[d][1,3]dioxole (4), and four non-alkaloid compounds, piperonylic acid (5), hesperidin (6), syringin (7), and β-sitosterol (8) were isolated from the stem bark of Zanthoxylum rhetsa grown in Vietnam. Their chemical structures were elucidated by spectroscopic analysis and compared with the references. Except for compound 6, all the remaining compounds (1–5, 7, and 8) were isolated for the first time from Z. rhetsa. The isolated compounds were tested for their cytotoxic activity against three human cancer cell lines, LU-1, Hep-G2, and KB. Compound 5 showed moderate cytotoxic activity against all three cell lines with IC50 values ranging from 48.13 to 49.06 µg mL−1. Notably, compound 6 demonstrated selective cytotoxicity against LU-1, Hep-G2, and KB cancer cell lines (IC50 66.48–67.41 µg mL−1) while non-toxic toward normal Vero cell. Compound 6 also exhibited its ability to inhibit main protease (Mpro) enzyme in vitro with an IC50 value of 55.49 µg mL−1 and in silico with the binding affinity toward targeted protein of −14.36 kcal mol−1.