Time-series remote sensing data can provide vegetation information in different stages in one growing period, which is very helpful for the understanding of the dynamic of land cover. As the basic data source of ChinaCover, the multi-spectral CCD images of HJ constellation have the same 30m spatial resolution and visible to near infrared band as other earth resource satellite. It can provide 2 days temporal resolution for there are two satellites named HJ-1A and HJ-1B with 180 degree phase differences and each satellite has 4 days temporal resolution. It is an important data source for the ecological land cover classification and eco-parameter inversion. However, incorrect geolocation caused by the satellite motion along the roll, pitch, yaw direction and the pixel displacement caused by the topographical variations at the off-nadir viewing angle are the bottlenecks when using the massive amount of HJ data. High precision space coordinates is the basic information to guarantee the information extraction, geostatistics analysis and to combine images with other geographic information. The geo-registration and orthorectification is the first issue facing in the pre-processing procedure for the remote sensing images. The newly launched small constellation of environmental and disaster mitigation (HJ-1A/B) are developed for the frequent natural disasters and environmental problems in China. It has been widely applied in the monitoring of the natural disasters, evaluating of the healthy condition of eco-environment and retrieval of surface parameters for its high spatio-temporal resolution and wide coverage. In order to satisfy the immense data processing requirements, this study constructed an auto-registration and orthorectification system for the HJ-1A/B CCD images according to the data characters. Compared with the general commercial software, the system of this study adopted an effectual method to kick out bad tie points to improve the efficiency and accuracy for the selection of tie points. At the same time, this system can fit the nadir tracking path for satellite to correct the pixel displacement caused by off-nadir viewing of topography. The accuracy of this system is evaluated from the validation points which automatically searched from the result and base image, and the validation points are grouped into four sub-regions in order to make a more objective validation for each region. According to statistics of the control points and validation points, the mean error before registration is 188.4m, and standard deviation error is 144.55m. After registration and orthorectification, the mean error and standard deviation error decreased to 40.59m and 21.39m separately. The systematic errors in the original images have been successfully eliminated in the final orthorectified results according to the comparison of spatial error distribution of validation points. The orbit operation rules for HJ1A/B will introduce the distortion on the geometric and spectral characters, and will further influence the time-series images construction because of the reduced overlay images in one revisit cycle. Cloud contamination is the main factors affected the tile points search and the coupled cloud detection algorithm and geometric correction algorithm will increase the geometric correction accuracy for cloudy satellite images and make them more useful. This system has been extensively used in the pre-processing procedure of HJ-1A/B CCD images for the LUCC mapping for the remote sensing survey and assessment project of the National Ecological Environment Decade of Change (2000-2010).