A variable rate fertilization controller based on CAN bus was presented. Firstly, variable rate fertilization control system and electro-hydraulic proportional valve-controlled motor rotation speed control system were introduced. Secondly, design of variable rate fertilization controller was described in detail including closed-loop PID control algorithm and communication protocol based on CAN bus. PID control parameters were determined through step response experiments and performance of closed-loop control system was analyzed. Variable rate fertilization control formula was deduced. Three kinds of fertilizers, urea ammonium phosphate and compound fertilizer, were used to test at different rotation speeds. Relationship equations between application rate of the three kinds of fertilizers and rotation speeds were calibrated. Finally, field experiments of fixed-rate and variable-rate fertilizations were conducted. Results show that the developed controller is suitable for variable rate application.