The cognitive decline caused by Alzheimer's disease (AD) is closely related to changes in the hippocampal structure captured by magnetic resonance imaging (MRI). To accurately analyze the morphological changes in the hippocampus caused by AD, it is necessary to extract the landmarks on the hippocampal surfaces which can ensure accurate registration between the different hippocampal surfaces, to eliminate morphological measurement errors caused by factors such as image acquisition, age, and gender. In this paper, we propose a method that can automatically extract the intrinsic landmarks of the hippocampal surfaces. More specifically, we use the eigen-graph of the hippocampal surfaces to extract the intrinsic and unified landmarks of all the hippocampal surfaces and calibrate along the longitudinal direction of the hippocampus surfaces along with the landmark correction for a few irregular hippocampal surfaces. Finally, we apply the extracted landmarks to the landmark-based registration algorithm, and the results show that landmark-based registration using our extracted landmarks can improve the accuracy of AD classification.