Autonomous planning of high-resolution optical earth-observing agile satellites requires on-orbit clouds detection over observation zones ahead, in order to reschedule the time window to enhance the operational effectiveness of satellites. Cloud heights are essential information, a cloud heights detection method for autonomous planning of satellites is proposed. On the basis of the difference in matching relationship between cloud and ground with different points remote sensing images, projecting deviation of cloud to ground is computed on the reference of ground and then cloud- top height is calculated by geometric relation. The simulation experimental result demonstrates that the disparity of cloud-top heights between detected and actual is less than 1 pixel and the method performs stably even rotation and affine transformation among images. Error analysis shows the trend of relative error along with different imaging angles. The experimental results of muti-angle imaging spectroradiometer images suggest that the proposed method has convincing performance over the real appilication.