The diary food factories in Japan are facing serious challenges of severe labor shortage and the increased diversity of demand. Food manufacturing companies are forced to improve factories to be more productive and flexible to deal with the expanding market scale in the future and also the product diversity. To improve the productivity and the flexibility, automation technologies have been implemented in manufacturing system with the popularization of Industrial 4.0 and Smart Factory. Based on the actual system construction practice of a dairy factory which is as a case study, this paper proposes a five-level horizontal model with automation technologies, aiming to realize high efficiency, rapid integration and relocation of the manufacturing system. This paper introduces the composition, the specifications and the functions of the horizontal model, and evaluates the function of each level. Finally, through the case study and numerical comparison on cost and labor hours, we verify the superiority of the proposed horizontal hierarchical system model for food factories.