We present here several advanced numerical methods, including both time-domain numerical methods and frequency-domain numerical methods, to numerically study the electromagnetic (EM) response of nonlinear graphene-based structures. In the case of time-domain method, we incorporate a nonlinear generalized source into the finite-difference time-domain (FDTD) method to study a wide frequency-range response of nonlinear graphene-based nanostructures. In the case of frequency-domain method, we would detail the approaches to solve the frequency-domain nonlinear coupling equations for EM modeling of nonlinear graphene-based nanostructure by using the finite element method (FEM) and coupled-mode theory (CMT). To verify the accuracy of the developed numerical methods, two numerical examples are given in the end.