In order to implement variable rate application control of intermittent spray based on pulse width modulation (PWM) technology, a blended pulse variable rate application controller was designed with its core part DSP56F805. The controller has two working modes. Operational parameters were set artificially in single mode, and received from upper computer through CAN bus in online mode. The controller can output 12 channels of PWM signal which can be adjusted individually. It also can monitor traveling speed of sprayer, rotational speed of diaphragm pump’s input shaft, spray pressure and application flow rates of each boom partition. In addition, the spray pressure can be regulated on line by predictive control algorithm with proportional relief valve. A variable rate application system was constructed by integration of a modified commercial boom sprayer and the controller, and its performance tests were carried out. Test results showed that the maximal effective frequency of the PWM signal was within 5 Hz, the ratio of flow regulation was more than 10, measuring error was within ±0.1 km/h for the traveling speed, within ±1.5 r/min for the rotational speed, within ±0.01 MPa for the spray pressure and within ±0.05 L/min for the flow rate, and regulating error of the spray pressure was within ±0.01 MPa in a 2 s regulating period.