Anaerobic hydrogen production (AHP) is a biochemical process capable of producing hydrogen and fatty acids from organic substrates in acidogenic phase. Currently, almost all of anaerobic systems use centrally stirred mixing where the flow is essentially rotated uniformly in the radial direction. Given the high energy requirement of mixing and the urgent needs for enhancing the contact between microbial particles and substrates, a new type of mixing strategy should be developed. This study focused on the enhancement of biogas production and organic removal efficiency in AHP systems through a novel chaotic mixing regime. The stirring impeller was operated eccentrically with the stirring center eccentrically located 2 and 4 cm off the center, respectively and at different heights (5, 10.5 and 16 cm). The eccentrically stirred mixing was expected to enhance the mixing efficiency and accelerate the contact between biomass and organic substrates in the AHP system. A numerical finite element model was developed to simulate the flow patterns and the biomass distribution, through which the Lyapunov exponent. values were calculated in order to assess the strength of eccentrically stirred mixing at different mixing eccentricities. The model simulations showed that at the height of 10.5 and 16 cm, the Lyapunov exponent. increased as the mixing eccentricity increased. This corresponded well with the experimental results, which showed that the organic removal efficiency and biogas production increased with the mixing eccentricity. Compared with centrally stirred mixing, eccentrically stirred mixing enhanced the interaction of flow and biomass particles and ultimately enhanced the biogas production and organic removal in AHP systems.