The precise construction of a hierarchical complex pattern on substrates is required for numerous applications. Here, a strategy to fabricate well-defined hierarchical three dimensional (3D) patterns on polymer substrate is developed. This technique, which combines photolithography and visible light-induced surface initiated living graft crosslinking polymerization (VSLGCP), can effectively graft 3D patterns onto polymer substrate with high fidelity and controllable height. Owing to the living nature of VSLGCP, hierarchical 3D patterns can be prepared when a sequential living graft crosslinking process is performed on the first formed patterns. As a proof-of-concept, a reactive two layer 3D pattern with a morphology of lateral stripe on vertical stripe is prepared and employed to separately immobilize model biomolecules, e.g., biotin and IgG. This two component pattern can specifically interact with corresponding target proteins successfully, indicating that this strategy has potential applications in the fabrication of polymer-based multicomponent biomolecule microarrays.