This study reports the strain-dependent efficiency of the InGaN-based multi-junction solar cell (MJSC) for the first time. The route of strain in MJSC is identified to be the results of dissimilar lattice constants between layers of sub-cell grown epitaxially with bandgap stepping. Utilising multi-layered strain model, the state of strain and its magnitude is evaluated for three types of MJSC structures referred to as MJSC-1, MJSC-2, and MJSC-3. It is found that the MJSC position-dependent strain is strongly dependent on the sub-cell thickness as well as on the number of sub-cells. Employing the MJSC position-dependent strain in combination with deformation potentials, strain-induced energy bandgap is calculated when imposed under tensile strain condition. Finally, the strain-dependent efficiencies of different MJSC structures are estimated and obtained to be lower with that of reported with strain effects over sighted. The loss of efficiency is identified to be due to the open circuit voltage which decreases under tensile strain condition. Among the MJSC structures studied here, MJSC-3 with 7-layers is less efficient and its efficiency decreases up to 3.01% when strain effect is taken into consideration.