The ability to use mechanical strain to steer chemical reactions creates completely new opportunities for solution‐ and solid‐phase synthesis of functional molecules and materials. However, this strategy is not readily applied in the bottom‐up on‐surface synthesis of well‐defined nanostructures. We report an internal strain‐induced skeletal rearrangement of one‐dimensional (1D) metal–organic chains (MOCs) via a concurrent atom shift and bond cleavage on Cu(111) at room temperature. The process involves Cu‐catalyzed debromination of organic monomers to generate 1,5‐dimethylnaphthalene diradicals that coordinate to Cu adatoms, forming MOCs with both homochiral and heterochiral naphthalene backbone arrangements. Bond‐resolved non‐contact atomic force microscopy imaging combined with density functional theory calculations showed that the relief of substrate‐induced internal strain drives the skeletal rearrangement of MOCs via 1,3‐H shifts and shift of Cu adatoms that enable migration of the monomer backbone toward an energetically favorable registry with the Cu(111) substrate. Our findings on this strain‐induced structural rearrangement in 1D systems will enrich the toolbox for on‐surface synthesis of novel functional materials and quantum nanostructures.