The growing complexity of modern hardware has created vast design spaces that are difficult to explore efficiently. Current design space exploration (DSE) methods treat designs as flat parameter vectors, failing to leverage the rich structural information inherent in hardware architectures. This paper presents a novel RTL hierarchy aware approach to microarchitecture DSE that exploits the natural structure of hardware designs. We propose an RTL hierarchy aware kernel that enables direct comparison of RTL hierarchies, preserving their structural characteristics. Our method incorporates module importance derived from hierarchical synthesis reports through a weighted kernel extension. Additionally, we introduce a clustering method that leverages the proposed kernel to identify distinct architectural patterns, enabling efficient parallel evaluation. Experimental results and ablation studies on a Gemmini-based RISC-V SoC demonstrate the superiority of our approach.