The effect of cementite structure on the mechanical properties of pearlite were investigated using molecular dynamics simulations. Three types of cementite structures were considered: single crystal, nanocrystalline, and a mixture of nanocrystalline and amorphous structures. The study found that regardless of the cementite structure, the ferrite phase in the pearlite exhibited plastic deformation first due to the activation of its internal {112} 〈111〉 slip system during tensile loading, resulting in macroscopic yielding of the pearlite. However, the difficulty of plastic deformation in the ferrite phase varied with different cementite structures. Compared to the other two types of cementite structures, the ferrite phase in the pearlite containing single crystal cementite exhibited the most difficult plastic deformation, leading to the highest peak stress. As the strain increased, the plastic deformation in the ferrite transferred through the ferrite-cementite interface to the cementite. After the plastic deformation transferred to the cementite, the different cementite structures exhibited distinct mechanical responses: the single crystal cementite structure experienced cleavage fracture, the nanocrystalline cementite structure underwent plastic deformation induced by grain boundary slip, while the nanocrystalline-amorphous mixture cementite structure showed shear deformation in the amorphous cementite and plastic deformation induced by grain boundary slip in the nanocrystalline cementite. Due to the influence of cementite mechanical response mechanism, the flow stress of the pearlite was minimal when the cementite in the pearlite were in single crystal structure. The study also revealed that when the cementite was in nanocrystalline structure, the flow stress of pearlite decreases with the grain size decreasing from 4.25 nm to 2.68 nm. When the cementite is a mixture of nanocrystalline and amorphous structure, the flow stress of pearlite decreases as the thickness of amorphous layer increases from 1 nm to 2 nm.