This paper derives a semi-discrete conservative difference scheme for the rotation-two-component Camassa–Holm system based on its Hamiltonian invariants. Mass, momentum and energy are preserved for the semi-discrete scheme. Furthermore, a fully discrete finite difference scheme is proposed without destroying any one of the conservative laws. Combining a nonlinear iteration with a threshold strategy, the accuracy of the scheme is guaranteed. Meanwhile, this scheme captures the formation and propagation of solitary wave solutions in long time behavior under smooth/nonsmooth initial data. Remarkably, a new type of asymmetric wave breaking phenomenon is revealed in the case of the nonzero rotational parameter.