Flow condensation in nanochannels is a high-efficiency method to deal with increasingly higher heat flux from micro/nanoelectronic devices. Here, we study the flow condensation heat transfer characteristics of nanochannels with different nanopillar cross-sectional areas and heights using molecular dynamics simulation. Results show that two phases containing vapor in the middle of the channel and liquid near walls can be distinguished by obvious interfaces when the fluid is at a stable state. The condensation performance can be promoted by adding nanopillars. With the increase in nanopillar cross-sectional areas or heights, the time that the fluid spends to reach stability will be put off, while the condensation performance enhances. Different from the small enhancement of nanopillar cross-sectional areas, the condensation heat transfer performance improves significantly at a higher nanopillar height, which increases the heat transfer rates by 11.6 and 35.8% when heights are 6a and 8a, respectively. The preeminent condensation heat transfer performance is ascribed to the fact that nanopillars with a higher height disturb the vapor-liquid interface and vapor region, which not only allows vapor atoms with strong Brownian motion to collide with nanopillar atoms directly but also increases deviations of vapor-liquid potential energy to facilitate condensation heat transfer in nanochannels.