Abstract: Variable pesticide application is one of the most important techniques for on-demand spraying. According to the prescription information or the online acquisition of the crop growth and disease occurrence, the forward speed of the unit can be detected to adjust the amount of pesticide application in real-time. The utilization efficiency of the insecticides or herbicides can be maximized to reduce the pollution caused by excessive pesticides to the environment. The residue of pesticide solutions can also be lowered in agricultural products. Among them, the pulse width modulation (PWM) variable spraying has been widely used at present, due to its short reaction time, high response speed, high atomization, and the large range of flow adjustment. Conventional nozzles can also be used to obtain better spray characteristics. However, the frequent hydraulic shocks can be caused by the solenoid valve switches, leading to the serious fluctuation of the pipeline pressure. Furthermore, the solenoid on/off latency and the alternating on/off action of adjacent nozzles can often occur in the PWM variable spray system. In this study, a suppression approach was proposed using staggered phase driving. A PWM variable control system was developed to support the various driving modes of the phase difference using a C37 controller. Additionally, a PWM variable spray platform was designed and constructed to incorporate the staggered phase driving. Subsequently, a series of tests were conducted on the PWM variable spray system, including the pressure fluctuation, atomization, and droplet deposition test. The results indicate that the staggered driving effectively reduced the amplitude and the coefficient of variation (CV) of the pressure fluctuation. There was no reduction, as the duty cycle increased. No significant difference was found in the average pressure of the system during phase driving. Once the duty cycle was 20% and 70%, the CV rates of the pressure fluctuation were -66.61% and -19.48%, respectively, for the 120° staggered- and same-phase systems. The least impact on the duty cycle's CV was observed in the phase difference between 60° and 90°. Furthermore, the smallest CV value of the pressure fluctuation was found at a phase difference of 120° across different duty cycles. The atomization tests reveal that the relative span (RS) of the droplets in the PWM variable spraying driven by a staggered phase was lower than that by the same phase. The RS decreased the most at the duty cycle of 50%, with a change rate of 5.56%. The deposition test shows that the CV of the droplet coverage in the staggered-phase PWM spray system was reduced by 31.75%, compared with the same phase driving. The staggered-phase driving mode can effectively reduce the non-uniform deposition caused by the low-frequency control of the PWM variable spraying. The finding can also offer technical support to further optimize the precision variable spraying.