The dynamic highprecision measurement of fertilizer application rate is a prerequisite for implementing variable fertilization. Although there are various methods for measuring fertilizer quality and flow in the field, there are still some problems such as inaccurate measurement and inability to adapt to the working environment when applying to the field. A microwave-based particle fertilizer mass flow measurement system was developed. A flow mass measurement model and method were proposed, and the agricultural granular fertilizer Stanley 15-15-15 and Sacokufu 15-15-15 were used as the experimental object. The microwave sensor distance and fertilizer discharge rate were controlled, and the data was smoothed by using a Kalman filter. The experiment achieved good results. The analysis of experimental data showed that the dominant frequency of the particle fertilizer echo signal was only related to the distance between the electric fertilizer discharge device and the sensor, while the power spectral density was only related to the number of fertilizer particles. By using the least squares method, the response relationship between the two compound fertilizers, Qt and Sval, was established. The determination coefficient R2 of the response relationship between the two types of compound fertilizers was not less than 0.9858, and the response relationships were validated. The measurement range for Sacokufu 15-15-15 was 1119.8~2065.9g/min, with a maximum measurement error of 6.35%. The measurement range for Stanley 15-15-15 was 1071.9~1877.9g/min, with a maximum measurement error of 4.85%. Its measurement performance fulfilled the operational needs of the task.