Porous scaffolds have widely been exploited in cartilage tissue regeneration. However, it is often difficult to understand how the delicate hierarchical structure of the scaffold material affects the regeneration process. Graphene materials are versatile building blocks for robust and biocompatible porous structures, enabling investigation of structural cues on tissue regeneration otherwise challenging to ascertain. Here, we utilize a graphene hydrogel with stable and tunable structure as a model scaffold to examine the effect of porous structure on matrix remodeling associated with ingrowth of chondrocytes on scaffolds. We observe much-accelerated yet balanced cartilage remodeling correlating the ingrowth of chondrocytes into the graphene scaffold with an open pore structure on the surface. Importantly, such an enhanced remodeling selectively promotes the expression of collagen type II fibrils over proteoglycan aggrecan, hence clearly illustrating that chondrocytes maintain a stable phenotype when they migrate into the scaffold while offering new insights into scaffold design for cartilage repair.