In our study, the dual time-stepping strategy of the gas-kinetic scheme is constructed and used for the simulation of unsteady flows. In comparison to the previous implicit gas-kinetic scheme, both the inviscid and viscous flux Jacobian are considered in our work, and the linear system of the pseudo-steady-state is solved by applying generalized minimal residual algorithm. The accuracy is validated by several numerical cases, the incompressible flow around blunt bodies (stationary circular cylinder and square cylinder), and the transonic buffet on the NACA0012 airfoil under hybrid mesh. The numerical cases also demonstrate that the present method is applicable to approach the fluid flows from laminar to turbulent and from incompressible to compressible. Finally, the case of acoustic pressure pulse is carried out to evaluate the effects of enlarged time step, and the side effect of enlarged time step is explained. Compared with the explicit gas-kinetic scheme, the proposed scheme can greatly accelerate the computation and reduce the computational costs for unsteady flow simulations.