As Very Large Scale Integration (VLSI) designs continue to scale in size and complexity, layout verification has become a central challenge in modern Electronic Design Automation (EDA) workflows. In practice, congestion can only be accurately identified after detailed routing, making traditional verification both time-consuming and costly. Learning-based approaches have therefore been explored to enable early-stage congestion prediction and reduce routing iterations. However, although prior methods incorporate both netlist connectivity and layout features, they often model the two in a loosely coupled manner and primarily produce numerical congestion estimates. We propose VeriHGN, a verification framework built on an enhanced heterogeneous graph that unifies circuit components and spatial grids into a single relational representation, enabling more faithful modeling of the interaction between logical intent and physical realization. Experiments on industrial benchmarks, including ISPD2015, CircuitNet-N14, and CircuitNet-N28, demonstrate that VeriHGN achieves the best or near-best performance over state-of-the-art methods in prediction accuracy and correlation metrics.