Molecular dynamics simulations are carried out to investigate the geometry effects of diatomic molecules on liquid flows in carbon nanotubes (CNTs). Oxygen molecules are considered as the fluid inside armchair (n,n) (n=6-20) CNTs. The simulated fluid temperature and bulk pressure for the liquid state are T=133 K and ρ_{b}=1346kg/m^{3}, respectively. In the agglomerated molecular cluster, nanoconfinement-induced structural changes are observed. As the CNT diameter decreases, it is confirmed that the flow rate significantly increases with irregular trends (discontinuity points in the profiles). From the discussion of the structure of the agglomerated fluid molecules, it is found that those trends are not simply caused by the structural changes. The main factor to induce the irregularity is confirmed to be the interlayer molecular movement affected by the combination of the molecular geometry and the arrangement of the multilayered structure.