To improve the hydrogen productivity and examine the hydrogen evolution mechanism of Clostridium paraputrificum, roles of formate in hydrogen evolution and effects of introducing formate-originated NADH regeneration were explored. The formate-decomposing pathway for hydrogen production was verified to exist in C. paraputrificum. Then NAD(+)-dependent formate dehydrogenase FDH1 gene (fdh1) from Candida boidinii was overexpressed, which regenerate more NADH from formate to form hydrogen by NADH-mediated pathway. With fdh1 overexpression, the hydrogen yield via NADH-involving pathway increased by at least 59 % compared with the control. Accompanied by the change of hydrogen metabolism, the whole cellular metabolism was redistributed greatly.