In order to achieve accurate measurement of fertilizer mass flow, a mass flow measurement system based on microwave Doppler method with a method for suppressing vibration interference was proposed. The velocity and concentration of the fertilizer particles were obtained from the Doppler signal of the granular fertilize, which was processed by using the fast Fourier transform, and the product of the velocity and concentration was defined as the sensor output value. Then, a linear regression model of the sensor output value and fertilizer mass flow was established by using the least squares method. By analyzing the statistical law of the signal, the five times mean value of power spectral density was used as the threshold to distinguish interference and signal. The fertilizer mass flow was changed by changing the rotating velocity of the fertilizing shaft. For laboratory environment, the mass flow of two types of fertilizers was measured. The experimental results showed that for two types of fertilizers, the max measurement value of the system can reach 2629.9g/min, and the relative errors of the microwave method were not more than 5%. In addition, the measurement system was installed on the fertilizing machine. An experiment was carried out by using the third type of fertilizer on the cement road beside the farmland. The analysis showed that the interference caused by vibration made the relative errors of measurement larger. The maximum relative error reached 21.57%. In order to improve the measurement accuracy, the proposed vibration interference suppression method was used. After the interference suppression, the fertilizer mass flow measurement range was between 1429.1g/min and 2976.9g/min, and the relative error was not more than 10.04%. The constructed system can accurately detect the mass flow of different fertilizers in the laboratory and under fertilizing machine conditions.