In this study, by using the nonequilibrium molecular dynamics and the kinetic theory, we examine the tailored nanoscale thermal transport via a gas-filled nanogap structure with mechanically-controllable nanopillars in one surface only, i.e., changing nanopillar height. It is found that both the thermal rectification and negative differential thermal resistance (NDTR) effects can be substantially enhanced by controlling the nanopillar height. The maximum thermal rectification ratio can reach 340% and the ∆T range with NDTR can be significantly enlarged, which can be attributed to the tailored asymmetric thermal resistance via controlled adsorption in height-changing nanopillars, especially at a large temperature difference. These tunable thermal rectification and NDTR mechanisms provide insights for the design of thermal management systems.