Computer-based geometry systems have been widely used for teaching and learning, but largely based on mouse-and-keyboard interaction, these systems usually require users to draw figures by following strict task structures defined by menus, buttons, and mouse and keyboard actions. Pen-based designs offer a more natural way to develop geometry theorem proofs with hand-drawn figures and scripts. This paper describes a pen-based geometry theorem proving system that can effectively recognize hand-drawn figures and hand-written proof scripts, and accurately establish the correspondence between geometric components and proof steps. Our system provides dynamic and intelligent visual assistance to help users understand the process of proving and allows users to manipulate geometric components and proof scripts based on structures rather than strokes. The results from evaluation study show that our system is well perceived and users have high satisfaction with the accuracy of sketch recognition, the effectiveness of visual hints, and the efficiency of structure-based manipulation.