In this study, optimization of hydrogen fermentation process from de-oiled Jatropha waste using a central composite design was modeled. A series of batch assays was performed at various substrate concentrations (32–368 g/L), temperatures (38–72°C) and pHs (4.8–8.2) according to the experimental design. The optimal conditions for cumulative hydrogen production (CHP) were determined by response surface methodology. The optimal substrate concentration, pH and temperature values were 211g/L, 6.5 and 55.4°C, respectively. Under these circumstances, the highest achievable CHP of 296 mL H2 was predicted. To validate the model, verification experiments were conducted. The results were satisfactorily matched with the statistically estimated values with peak CHP value of 307.4 ± 4.5mL H2. Microbial community profiling (PCR-DGGE) has revealed that the dominant bacterial community present belonged to Clostridium thermopalmarium, Clostridium buytricum, Bacillus ginsengihumi and Bacillus coagulans.