This paper presents a modified Runge-Kutta (MRK) scheme for the generalized Benjamin-Bona-Mahony-Burgers equation. The MRK method separate this equation into two parts which apply different finite difference scheme in space, and finally use fourth-order Runge-Kutta method in time.The scheme is conditionally stable and convergent with order of O(tau(4) + h(2)), the Comparisons of the existing numerical methods demonstrate that this scheme is capable of high accuracy and stability.