Owing to its high porosity, specific surface area and three-dimensional structure, three-dimensional graphene (3D-C) is a promising scaffold material for tissue engineering, regenerative medicine as well as providing a more biologically relevant platform for living organisms in vivo studies. Recently, its differentiation effects on cells growth and anti-inflammation properties have also been demonstrated. Here, we report a complete study of 3D-C as a fully adequate scaffold for tissue engineering and systematically analyze its biocompatibility and biodegradation mechanism. The metabolic activities of liver cells (HepG2 hepatocarcinoma cells) on 3D-C are studied and our findings show that cell growth on 3D-C has high cell viability (> 90%), low lactate production (reduced by 300%) and its porous structure also provides an excellent oxygenation platform. 3D-C is also biodegradable via a 2-step oxidative biodegradation process by first, disruption of domains and lift off of smaller graphitic particles from the surface of the 3D-C and subsequently, the decomposition of these graphitic flakes. In addition, the speed of the biodegradation can be tuned with pretreatment of O2 plasma.