In order to solve the problem in traditional protected agriculture, namely the inefficient use of water and fertilizer, less information collection, weak capability of data mining and implementation, an intelligent cloud irrigation system was proposed based on the technology of dualline decoding and cloud computing to integratively manage water and fertilizer for protected agriculture, which was composed of intelligent cloud irrigation control system, automatic machine of integration of water and fertilizer, water saving irrigation system with high efficient. The system via dualline decoding technology, and a variety of sensors were used to collect the parameters of crop growth environment for each individual protected agriculture in realtime. Then all kinds of collected data were timely transmitted and stored in cloud data management platform. Thereafter, the ability of calculation and analysis from cloud calculated cluster was used, water and fertilizer needs, irrigation and fertilization system in protected agriculture under different environmental conditions for crop growth were scientifically determined to achieve intelligent control of water and fertilizer integration. The system was of great importance in guiding protected agriculture to achieve high yield, high quality, ecology and safety in production. Two application examples in planting bases of protected agriculture showed that compared with the traditional irrigation methods, the intelligent cloud irrigation system based on the technology of dualline decoding and cloud computing to manage integrated water and fertilizer for protected agriculture can improve the water use efficiency by 25%~40% and fertilizer use efficiency by 15%~35%, which shortened labor time and decreased labor force sharply.