The Ice-sheet and Sea-level System Model (ISSM) provides solutions for Stokes equations relevant to ice sheet dynamics by employing finite element and fine mesh adaption. However, since its finite element method is compatible only with Central Processing Units (CPU), the ISSM has limits on further economizing computational time. Thus, by taking advantage of Graphics Processing Units (GPUs), we design a graph convolutional network (GCN) as a fast emulator for ISSM. The GCN is trained and tested using the 20-year transient ISSM simulations in the Pine Island Glacier (PIG). The GCN reproduces ice thickness and velocity with a correlation coefficient greater than 0.998, outperforming the traditional convolutional neural network (CNN). Additionally, GCN shows 34 times faster computational speed than the CPU-based ISSM modeling. The GPU-based GCN emulator allows us to predict how the PIG will change in the future under different melting rate scenarios with high fidelity and much faster computational time.