Nanorods are promising components of energy and information storage devices that rely on solute-driven phase transformations, due to their large surface-to-volume ratio and ability to accommodate strain. Here we investigate the hydrogen-induced phase transition in individual penta-twinned palladium nanorods of varying aspect ratios with ~3 nm spatial resolution to understand the correlation between nanorod structure and thermodynamics. We find that the hydrogenated phase preferentially nucleates at the rod tips, progressing along the length of the nanorods with increasing hydrogen pressure. While nucleation pressure is nearly constant for all lengths, the number of phase boundaries is length-dependent, with stable phase coexistence always occurring for rods longer than 55 nm. Moreover, such coexistence occurs within individual crystallites of the nanorods and is accompanied by defect formation, as supported by in situ electron microscopy and elastic energy calculations. These results highlight the effect of particle shape and dimension on thermodynamics, informing nanorod design for improved device cyclability.