Crop yield estimation is important for formulating informed regional and national food trade policies. The introduction of remote sensing in agricultural monitoring makes accurate estimation of regional crop yields possible. However, remote sensing images and crop distribution maps with coarse spatial resolution usually cause inaccuracy in yield estimation due to the existence of mixed pixels. This study aimed to estimate the annual yields of maize and sunflower in Hetao Irrigation District in North China using 30 m spatial resolution HJ-1A/1B CCD images and high accuracy multi-year crop distribution maps. The Normalized Difference Vegetation Index (NDVI) time series obtained from HJ-1A/1B CCD images was fitted with an asymmetric logistic curve to calculate daily NDVI and phenological characteristics. Eight random forest (RF) models using different predictors were developed for maize and sunflower yield estimation, respectively, where predictors of each model were a combination of NDVI series and/or phenological characteristics. We calibrated all RF models with measured crop yields at sampling points in two years (2014 and 2015), and validated the RF models with statistical yields of four counties in six years. Results showed that the optimal model for maize yield estimation was the model using NDVI series from the 120th to the 210th day in a year with 10 days’ interval as predictors, while that for sunflower was the model using the combination of three NDVI characteristics, three phenological characteristics, and two curve parameters as predictors. The selected RF models could estimate multi-year regional crop yields accurately, with the average values of root-mean-square error and the relative error of 0.75 t/ha and 6.1% for maize, and 0.40 t/ha and 10.1% for sunflower, respectively. Moreover, the yields of maize and sunflower can be estimated fairly well with NDVI series 50 days before crop harvest, which implicated the possibility of crop yield forecast before harvest.