The molecular arrangement of functional chromophores is essential to construct functional nanomaterials. Synthetic DNA has been used as a structural scaffold to control and construct molecular assembly. We now describe the formation of artificial DNA/porphyrin complexes where porphyrins working as photoactive molecules were placed at specific locations on the DNA through a non‐covalent interaction. Spectroscopic analysis by UV/vis, circular dichroism (CD), and melting temperature measurements showed that the binding of water‐soluble porphyrin derivatives with methylpyridinium groups (TMPyP and DMPyP) to DNA can be directed by hydrophobic cavities composed of a pair of abasic site analogs (dS). CD measurements showed that the two porphyrins can be accommodated at two specific sites when the DNA molecule had two cavities, as evidenced by the exciton‐coupled CD spectra of the porphyrins. Photoelectrochemical experiments showed that the DNA complexes accommodating DMPyP at specific locations can respond to light excitation to generate a photocurrent when immobilized on the electrode surface. Our results demonstrated that the control of the porphyrin binding using the dS/dS pair is a useful approach to construct artificial DNA with porphyrin molecules, leading to the design of photoresponsive materials and photoelectrochemical sensors.