When the Gaussian kernel function is chosen with a small kernel bandwidths, the minimum error entropy Kalman filter (MEEKF) exhibits excellent performance. However, further narrowing the kernel bandwidths leads to a degradation in performance. To address this issue, this paper proposed a Graph-based MEEKF (G-MEEKF) algorithm based on Graph Signal Processing (GSP) theory. The G-MEEKF algorithm addresses the problem by smoothing the errors using graph filtering and incorporating graph topology into the cost function. The convergence of the algorithm is theoretically analyzed and simulations demonstrate that G-MEEKF improves the performance of MEEKF under small kernel bandwidths. Furthermore, it is emphasized that the topology of the graph abstracted from the minimum error entropy (MEE) definition also influences the performance of the algorithm.