The present invention provides an intelligent pure water / ultra-pure water preparing system and an automatic control method thereof, which comprises the steps of pretreating, medicine adding, film filtering, sterilizing and disinfecting to the water. The invention is characterized in that: the full flow from the raw water inlet to the pure water product is designed with modules, and the whole process flow is composed of a pretreating module, a constant temperature module, an anti-penetration primary desalting module, an EDI advanced desalting module, a physical sterilizing module, a TOC decomposing module, a degassing module, a temperature regulating module and a water-quality fine-processing module which are sequentially connected in series; the operation of each stage of module in the flow adopts a distributed automatic control system, the centralized management and three-stage control of distributed control to the operation condition of each process flow module are realized through PC technology with the field bus. The system of the invention is designed to an integrated device, and the modularized designing of the full flow is designed to a state that the modules can be added ordeleted randomly without affecting the operation of the whole system. The intelligent pure water / ultra-pure water preparing system has high flexibility in the application aspect and has the advantages of compact structure, construction quality increase, shortened construction period, etc.