In this paper, we investigate the performance of large-sized single-walled carbon nanotubes (SWCNTs) incorporated with mono vacancy (MV), double vacancy (DV), and Stone-Wales (SW) topological defects as a medium for hydrogen adsorption using molecular dynamics (MD) simulations. A novel potential energy distribution (PED) method is employed with MD simulations to determine the adsorbed hydrogen molecules and associated binding energy. In addition, we extended our work to bundles of defected SWCNT (D-SWCNT) that provided the most prominent adsorption capacity subjected to temperature and pressure variations. In particular, four representative (8,8), (13,13), (19,19), and (33,0) SWCNTs are simulated under various thermodynamic conditions, and collected adsorption isotherms data reveals higher gravimetric density for large-sized SWCNT. At 77 K and 100 bar, the maximum hydrogen uptake in pristine SWCNTs is 6.88–7.73 wt%, depending on the size of the nanotubes. In contrast, the binding energy decreases as the nanotube size increases. At 77 K, (8,8) and (19,19) SWCNTs have average binding energies of 0.043 and 0.021 eV, respectively. Meanwhile, (19,19) SWCNT incorporated with 1% DV defects having 5–8 rings (DV1) and MV defects yields the maximum storage capacity of 9.07 wt% and 8.62 wt%, respectively, at 77 K. Furthermore, the increment of about 43.29% in wt.% is obtained for DV1 defected nanotube relative to pristine SWCNT at 300 K and 100 bar. Moreover, our results indicate the maximum hydrogen uptake of 8.65, 7.15, 2.57, and 1.33 wt% in the square array of DV1 defect embedded SWCNTs at 77, 100, 200, and 300 K, respectively, compared to 9.07, 6.65, 2.24, and 1.11 wt% in the isolated D-SWCNT at identical conditions. As a result, the D-SWCNT bundles are better suited for hydrogen storage at high temperatures than the isolated D-SWCNT. Our present study paves the way to progress toward the efficient usage of D-SWCNTs with few chemical alterations for scaled-up applications.