<p>This paper introduces a novel hybrid model of natural computing, termed the hyper-edge replacement graph rewriting PR system, by synergistically combining the principles of reaction systems with the hyper-edge replacement graph rewriting P system. Inspired by biological cells, this model leverages hierarchical membrane structures to encapsulate regions operating as reaction systems, facilitating complex biochemical interaction modeling. By integrating facilitation and inhibition mechanisms with graph generation capabilities, this framework expands the capabilities of both paradigms, offering a powerful tool for simulating and analyzing complex graph-based structures. The properties and dynamics of this innovative model are explored, demonstrating its potential for advancing natural computing research. A comparative analysis with existing model further demonstrate its efficacy and broader applicability.</p>