A functional hydrogen producing consortium was isolated from soil by heat pre-treatment technique and hydrogen production at different substrate concentration was evaluated. The forest soil was heat pre-treated at 65, 80, 95, 105 and 120 °C temperature for 1 h. As revealed by PCR-DGGE analysis and hydrogen yield, the hydrogen producing microbial community changed with increase in heat pre-treatment temperatures giving potential hydrogen producing consortium at 95–105 °C soil pre-treatment. The maximum hydrogen production rate, hydrogen yield and cumulative hydrogen with 15–20 g glucose were 1390–1576 mL/L/day, 1.83–1.93 mol H2/mol glucose, and 2966–3146 mL H2/L, respectively. The metabolic pathways shifted from ethanol-type to acetate–formate type as soil pre-treatment temperature increased from 65 to 120 °C. The soil heat pre-treatment approach is effective for isolating hydrogen producing natural Clostridium consortium from the soil as enumerations of the functional strains need specific temperature range to florish.