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Recently, the production of vegetables, flowers, and spices in greenhouses has been experiencing accelerated growth in China. In greenhouse cultivation, the fertigation system plays an essential role in the supply of water and nutrient elements for crops. In this paper, an automatic control system for greenhouse fertigation based on fuzzy PID algorithm was designed and implemented. In this system, the concentrated fertilizer solutions (included acid or alkali) were injected into the fertilizer mixing tank by Venturi. The flow rate of concentrated fertilizer solution was regulated by a solenoid valve with pulse-width modulation (PWM) method. By building an accurate flow measurement device, the relations between the flow rate of Venturi and the pulse-width modulation (PWM) parameters of solenoid valve was explored. The relations between the electrical conductivity (EC) and pH values of the mixed nutrient solution and the concentrated fertilizer solution (acid/ alkali) volume were found. A fuzzy PID control algorithm was put forward to accurate regulate the fertilizer component ratio and the EC /pH value of the nutrient solution. Full circuit and program codes were implemented and the performance of the control system was test. The test results show that the control method is reasonable, the system runs reliably, and can satisfy the requirements of precise fertigation in greenhouse.