A graphene nanodots-encaged porous gold electrode via ion beam sputtering deposition (IBSD) for electrochemical sensing is presented. The electrodes were fabricated using Au target, and a composite target of Al and graphene, which were simultaneously sputtered onto glass substrates by Ar ion beam, followed with hydrochloric acid corrosion. The as-prepared graphene nanodots-encaged porous gold electrodes were then used for the analysis of heavy metal ions, e.g. Cu2+ and Pb2+ by Osteryoung square wave voltammetry (OSWV). These porous electrodes exhibited enhanced detection range for the heavy metal ions due to the entrapped graphene nanodots in 3-D porous structure. In addition, it was also found that when the thickness of porous electrode reached 40 nm the detection sensitivity came into saturation. The linear detection range is 0.009-4 μM for Cu2+ and 0.006-2.5 μM for Pb2+. Good reusability and repeatability were also observed. The formation mechanism and 3-D structure of the porous electrode were also investigated using scanning electron microscope (SEM), transmission electron microscope (TEM) and X-ray photoelectron spectra (XPS). This graphene entrapped 3-D porous structure may envision promising applications in sensing devices.