Accurately obtaining crop yields is an important part of the precision agriculture technology system; with the increased mechanisation of cotton planting and harvesting, it has become particularly important to accurately obtain seed cotton yield data. In order to achieve accurate estimation of machine-picked seed cotton yield, this paper designs a machine-picked seed cotton yield estimation system based on microwave Doppler principle. Based on LabVIEW software, the signal acquisition circuit is designed; the power spectrum of the echo signal is estimated; the signal echo power is obtained; the relationship model between echo power and seed cotton mass is established by using multiple regression equations; and the reliability of the model is verified by using statistical methods. By adjusting the rotational speed of the fan, the wind speed at the inlet of the cotton pipeline was 10 m/s, 15 m/s and 20 m/s, and the yield estimation tests were carried out at the three wind speeds, and the data showed that the average absolute percentage errors of the estimation at the three wind speeds were 7.36%, 7.72% and 8.17%, and the mean squared errors were 2.699, 4.938 and 4.026, respectively. The test results show that the accuracy of seed cotton mass estimation under the three wind speeds basically meets the needs of the yield measurement system, and the systematic error of seed cotton yield estimation is the smallest when the wind speed is 10 m/s.