The hydrolysis and acidogenesis were the rate-controlling steps in the overall anaerobic digestion (AD) process. Considering the optimum conditions for different AD stage were diverse, the development of multi-stage AD system was likely to enhance each stage of AD through optimizing control respectively. This study developed a highly integrate three-stage anaerobic digester (HM3) to bond the advantages of dry AD and wet AD for anaerobic co-digestion of food waste and horse manure. The digester design was mainly comprised of three chambers i.e. high-solids hydrolysis stage, high-solids acidogenesis stage and wet methanogensis stage. Through comparing the treatment performance with other two control digesters, HM3 presented 11.2 ~22.7% higher methane yield. The improved methane yield was mainly attributed to the functionalized partitioning in this integrated digester, which significantly accelerated the solubilization of solid organic matters and the formation of organic acids as well as ammonia in the high-solids hydrolytic and acidogenic stage respectively. Additionally, HM3 also showed the highest volatile solids reduction rate among the three digesters. Real-time PCR and pyrosequencing analysis indicated that the abundance and biodiversity of microorganisms including bacteria and archaea in HM3 was much higher than that in the control reactors. Moreover, different dominant bacterial communities with various functions were enriched in the high-solids hydrolytic stage e.g. Lactobacillaceae and Pseudomonadaceae, acidogenetic stage e.g. Porphyromonadaceae and Enterobacteriaceae and wet methanogenic stage e.g. Aminobacterium, Clostridium and Proteiniphilum. The bioaugmentation and functional partition in this three-stage anaerobic digester enhanced the transformation from particulate organic matter to soluble substrate and methanogenesis, which is meaningful for its application in practice.