Electronic transport properties of a pristine C₆ chain and Si/B-substituted into the C₆ chain sandwiched between two (5, 5) capped carbon nanotube electrodes were investigated through first-principles calculations based on non-equilibrium Green's functions (NEGF) conjugated with density functional theory (DFT). Si and B substitutions will affect the I–V curve of a pristine C₆ chain. In the I–V characteristics, multi negative differential resistance (NDR) with large peak to valley ratio (PVR) and rectifying actions were observed. The NDR behavior originates from the joining and moving of conduction orbitals inside and outside of the bias window at a certain bias voltage. Furthermore, the assessment of transmission coefficient and distribution of molecular orbitals reveals that the rectifying performance is the result of the asymmetric distribution of the frontier molecular orbitals in the central region and their coupling with the electrodes. Multi NDR behavior of B substitution under very low bias voltage is a unique property of our proposed devices. Moreover, the CNT|C–(B–C)₂–C|CNT molecular device shows a high PVR up to 31.8, which demonstrates that the proposed devices can be useful for molecular switching in nanoelectronic devices.