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The accurate and timely estimation of regional crop biomass at different growth stages is of great importance in guiding crop management decision making. The recent availability of long time series of remote sensing data offers opportunities for crop monitoring. In this paper, four machine learning models, namely random forest (RF), support vector machine (SVM), artificial neural network (ANN), and extreme gradient boosting (XGBoost) were adopted to estimate the seasonal corn biomass based on field observation data and moderate resolution imaging spectroradiometer (MODIS) reflectance data from 2012 to 2019 in the middle reaches of the Heihe River basin, China. Nine variables were selected with the forward feature selection approach from among twenty-seven variables potentially influencing corn biomass: soil-adjusted total vegetation index (SATVI), green ratio vegetation index (GRVI), Nadir_B7 (2105–2155 nm), Nadir_B6 (1628–1652 nm), land surface water index (LSWI), normalized difference vegetation index (NDVI), Nadir_B4 (545–565 nm), and Nadir_B3 (459–479 nm). The results indicated that the corn biomass was suitably estimated (the coefficient of determination (R2) was between 0.72 and 0.78) with the four machine learning models. The XGBoost model performed better than the other three models (R2 = 0.78, root mean squared error (RMSE) = 2.86 t/ha and mean absolute error (MAE) = 1.86 t/ha). Moreover, the RF model was an effective method (R2 = 0.77, RMSE = 2.91 t/ha and MAE = 1.91 t/ha), with a performance comparable to that of the XGBoost model. This study provides a reference for estimating crop biomass from MOD43A4 datasets. In addition, the research demonstrates the potential of machine learning techniques to achieve a relatively accurate estimation of daily corn biomass at a large scale. [ABSTRACT FROM AUTHOR]