In Mongolia, the monitoring and estimation of spring wheat yield at the regional and national levels are key issues for the agricultural policy and food management as well as for the economy and society as a whole. The remote sensing data and technique have been widely used for the estimation of crop yield and production in the world. For the current research, nine remote sensing indices were tested that include normalized difference drought index (NDDI), normalized difference water index (NDWI), vegetation condition index (VCI), temperature condition index (TCI), vegetation health index (VHI), normalized multi-band drought index (NMDI), visible and shortwave infrared drought index (VSDI), and vegetation supply water index (VSWI). These nine indices derived from MODIS/Terra satellite have so far not been used for crop yield prediction in Mongolia. The primary objective of this study was to determine the best remote sensing indices in order to develop an estimation model for spring wheat yield using correlation and regression method. The spring wheat yield data from the ground measurements of eight meteorological stations in Darkhan and Selenge provinces from 2000 to 2017 have been used. The data were collected during the period of the growing season (June–August). Based on the analysis, we constructed six models for spring wheat yield estimation. The results showed that the range of the root-mean-square error (RMSE) values of estimated spring wheat yield was between 4.1 (100 kg ha−1) to 4.8 (100 kg ha−1), respectively. The range of the mean absolute error (MAE) values was between 3.3 to 3.8 and the index of agreement (d) values was between 0.74 to 0.84, respectively. The conclusion was that the best model would be (R2 = 0.55) based on NDWI, VSDI, and NDVI out of the nine indices and could serve as the most effective predictor and reliable remote sensing indices for monitoring the spring wheat yield in the northern part of Mongolia. Our results showed that the best timing of yield prediction for spring wheat was around the end of June and the beginning of July, which is the flowering stage of spring wheat in this study area. This means an accurate yield prediction for spring wheat can be achieved two months before the harvest time using the regression model.