Planar micro-supercapacitors (MSCs) have drawn extensive research attention owing to their unique structural design and size compatibility for microelectronic devices. Graphene has been widely used to improve the performance of microscale electrochemical capacitors. However, investigations of an intrinsic electrochemical mechanism for graphene-based microscale devices are still not sufficient. Here, micro-supercapacitors with various typical architectures are fabricated as models to study the graphene effect, and their electrochemical performance is also evaluated. The results show that ionic accessibility and adsorption are greatly improved after the introduction of the holey graphene intermediate layer. This study provides a new route to understand intrinsic electrochemical behaviors and possesses exciting potential for highly efficient on-chip micro-energy storage.