A series of new 5‐morpholino‐thiophene‐indole/oxindole hybrids has been designed and synthesized using molecular hybridization approach. The synthesized compounds were evaluated for their in vitro cytotoxic potential against selected human cancer cell lines such as triple negative breast (MDA‐MB‐231), liver (SK‐Hep‐1), breast (MCF‐7), colon (HCT‐116) mouse melanoma (B16F10) and compared with normal human lung epithelial cell line (BEAS‐2B). Among the tested hybrids 11a–o and 13a–d, the compound 11f [(Z)‐N′‐((1‐Benzyl‐1H‐indol‐3‐yl)methylene)‐5‐morpholino‐4‐(p‐tolyl)thiophene‐2‐carbohydrazide] showed significant cytotoxic activity on HCT‐116 cancer cell line with IC50 value of 8.98 ± 0.6 μM. Cell cycle analysis revealed that compounds arrested the cell cycle in sub‐G1 phase. Moreover, JC‐1, acridine orange, DAPI nucleic acid, DCFDA staining studies suggest that one of the representative compound 11 f inhibited the cell proliferation through apoptosis. Further, molecular docking and relative viscosity studies of 11 f indicated the minor groove binding towards CT‐DNA.