The source of raw materials for hydrogen production can be expanded by using vine waste as a substrate. Likewise, the effectiveness of vine waste can also be improved. However, plant parts such as stems and leaves often differ in physicochemical properties, which significantly affects the effectiveness of biochemical transformation. In this research, sweet potato was used as substrate in photo-fermentative hydrogen production (PFHP) to evaluate differences in bio-hydrogen production yield potential and energy conversion efficiency for its stem and leaf. Physicochemical properties were determined using the following techniques: elementary analysis, SEM, and X-ray diffraction. The Gompertz model was adopted to analyze the kinetic parameters, and energy conversion efficiency was calculated. The results showed that stem samples with loose structures produced more hydrogen, with a total cellulose and hemicellulose content of 44.6%, but crystallinity was only 29.67%. Cumulative bio-hydrogen yield of stem was 66.03 mL/g TS, which was 3.59 times higher than that of leaf. An increase of 258.93% in energy conversion efficiency was obtained when stem was used for PFHP. In conclusion, stem samples were more suitable for PFHP than leaf samples.