Phenine nanotubes (PNTs) have recently been synthesized as a promising new one-dimensional material for high-performance electronics. The periodically distributed vacancy defects in PNTs result in novel semiconducting properties, but may also compromise their mechanical properties. However, the role of these defects in modifying the structural and mechanical properties is not yet well understood. To address this, we conducted systematic molecular dynamics simulations investigating the structural evolution and mechanical responses of PNTs under various conditions. Our results demonstrated that the twisting of linear carbon chains in both armchair and zigzag PNTs led to interesting structural transitions, which were sensitive to chiralities and diameters. Additionally, when subjected to tensile and compressive loading, PNTs’ cross-sectional geometry and untwisting of linear carbon chains resulted in distinct mechanical properties compared to carbon nanotubes. Our findings provide comprehensive insights into the fundamental properties of these new structures while uncovering a new mechanism for modifying the mechanical properties of one-dimensional nanostructures through the twisting–untwisting of linear carbon chains.