Edible fruit waste has been studied and considered to be the ideal substrates for low-cost bio-H2 production. However, the garden waste of ornamental plant fruits, which has similar components to edible fruit, is rarely studied. In this study, the potential and characteristics of fermentative bio-H2 production from the campus ornamental plant fruit of Malus prunifolia (MP) in both ethanol- and butyrate-types were investigated. Ethanoligenens harbinense B49 and Clostridium neuense G1 were employed as the inoculums for the ethanol- and butyrate-type fermentations, respectively. The results indicated that the fruit of MP is rich in fructose and sucrose, both of strains B49 and G1 could grow well with MP powder as the carbon source for fermentation. However, a higher H2 yield of 1.77 mol-H2/mol-hexose was obtained in the butyrate-type fermentation with strain G1, which was 1.4 times of that with strain B49. C. neuense G1 was more suitable for the H2 fermentation with MP as substrate, and a H2 yield of 0.55 mol-H2/mol-hexose by strain B49 was observed in the test of buffer system exchanging from ethanol-type to the butyrate-type. In summary, garden wastes such as fruits of ornamental plants should be given more attention as low-cost fermentation substrate candidates for bio-H2 production.