We demonstrate that the directed self-assembly of AB diblock copolymers by periodic trenches can be used to fabricate large-scale ordered hybrid line-dot nanopatterns in addition to a defect-free dot nanopattern. The formation of line or dot nanopatterns in thin films with proper surface affinities is controlled by the film thickness, which is modulated by a topographic pattern consisting of steps and trenches. Two kinds of line-dot nanopatterns are achieved with cylinder-forming and sphere-forming copolymers, respectively. One kind of hybrid nanopatterns is composed of perpendicularly standing cylinders (dots) on the steps and parallel monolayer cylinders (lines) within the trenches, while the dots of the other kind are replaced by monolayer spheres on the steps. The thermodynamic stability region of target hybrid nanopatterns is identified by constructing two-dimensional phase diagrams with respect to two control parameters of step height and film thickness using self-consistent field theory. Furthermore, a process window of the line-dot nanopatterns is estimated using cell dynamics simulations based on time-dependent Ginzburg-Landau theory, confirming their feasibility in kinetics.