We performed molecular dynamics simulations with a coarse-grained model to investigate the capillary filling dynamics of polymer chains in nanopores. Short chains fill slower than predicted by the Lucas−Washburn equation, but long chains fill faster. The analysis shows that the combination of the confinement effect on the free energy of chains and the reduction of the effective radius due to the "dead zone" slows down the imbibition. Reduction of the entanglements is the main factor behind the reversing dynamics because of the lower effective viscosity, which leads to a faster filling. This effect is enhanced in the smaller capillary and more profound for longer chains. The observed increase in the mean-square radius of gyration during capillary filling provides a clear evidence of chain orientation, which leads to the decrease in the number of entanglements. For the scaling relation between the effective viscosity and the degree of polymerization, we find the exponent will increase in the larger nanopore.