The pH value regulating control process has the characteristics of nonlinearity, pure hysteresis, time degeneration and uncertainty in the precision fertigation system. A model described the pH value regulating process was established. The cloud model is a model that can deal with the uncertain transition between qualitative concepts and quantitative description. Based on this, a control algorithm with cloud inference in the variable universe fuzzyPI controller (CVFPI) was proposed. In this algorithm, the normal cloud model was used to describe certain language concept corresponding to the system error and error rate. The inference of rule premise was realized by X conditional membership cloud while the inference of rule post was realized Y conditional membership cloud. A set of stretching factors with proportional exponential function was used to modify the universe of input and output variable real time, and a two dimensional inference engine based on cloud model was designed to adjust control parameters of PI controller on line. In order to verify the effectiveness and superiority of the proposed algorithm, the test platform of pH control process of the fertigation equipment was constructed. Two simulation experiments and two field experiments were carried out using CVFPI, VFPI and PI control algorithm respectively. The contrast testing results demonstrate that the proposed CVFPI control algorithm can meet the requirements of pH process control in the precision fertigation system, it has better characteristics both in dynamic process and steady state. Compared to PI and VFPI, CVFPI has smaller overshoot, shorter stable time and stronger ability of antiinterference.