Heliotropium is a genus of the Boraginaceae family. Its members are used in many traditional and folklore medicines to treat several ailments. Despite this widespread usage, only a few evidence-based scientific studies investigated and identified its phytoconstituents. Herein, we documented the chemical profile of the Heliotropium ramosissimum methanolic extract using gas chromatography-mass spectrometry (GC–MS) and liquid chromatography-tandem mass spectrometry (LC–ESI–MS/MS) and assessed its antioxidant and cytotoxic effects. The methanolic extract exhibited high phenolic content (179.74 ± 0.58 µg/mL) and high flavonoid content (53.18 ± 0.60 µg/mL). The GC–MS analysis of the lipoidal matter allowed us to identify 41 compounds with high percentages of 1,2-benzenedicarboxylic acid, bis(2-methoxyethyl) ester (23.91%), and 6,10,14-trimethylpentadecan-2-one (18.74%). Thirty-two phytomolecules were tentatively identified from the methanolic extract of H. ramosissimum using LC–MS/MS. These compounds belonged to several phytochemical classes such as phenolic acids, alkaloids, coumarins, and flavonoids. Furthermore, we assessed the antioxidant activity of the methanolic extract by DPPH assay and oxygen radical absorbance capacity assay, which yielded IC50 values of 414.30 µg/mL and 170.03 ± 44.40 µM TE/equivalent, respectively. We also assessed the cytotoxicity of the methanolic extract on seven different cell lines; Colo-205, A-375, HeLa, HepG-2, H-460, and OEC showed that it selectively killed cancer cells with particularly potent cytotoxicity against Colo-205 without affecting normal cells. Further studies revealed that the extract induced apoptosis and/or necrosis on Colo-205 cell line at an IC50 of 18.60 µg/mL. Finally, we conducted molecular docking on the LC–ESI–MS/MS-identified compounds against colon cancer antigen 10 to find potentially cytotoxic compounds. Binding score energy analysis showed that isochlorogenic acid and orientin had the highest affinity for the colon cancer antigen 10 protein, with binding scores of (− 13.2001) and (− 13.5655) kcal/mol, respectively. These findings suggest that Heliotropium ramosissimum contains potent therapeutic candidates for colorectal cancer treatment.