We investigate the effects of the vacancy defects (i.e., missing atoms) in carbon nanotubes (CNTs) on the interfacial shear strength (ISS) of the CNT-polyethylene composite with the molecular dynamics simulation. In the simulation, the crystalline polyethylene matrix is set up in a hexagonal array with the polymer chains parallel to the CNT axis. Vacancy defects in the CNT are introduced by removing the corresponding atoms from the pristine CNT (i.e., CNT without any defect). Three patterns of vacancy defects with three different sizes are considered. Two types of interfaces, with and without cross-links between the CNT and the matrix are also considered here. Polyethylene chains are used as cross-links between the CNT and the matrix. The Brenner potential is used for the carbon-carbon interaction in the CNT, while the polymer is modeled by a united-atom potential. The nonbonded van der Waals interaction between the CNT and the polymer matrix and within the polymer matrix itself is modeled with the Lennard-Jones potential. To determine the ISS, we conduct the CNT pull-out from the polymer matrix and the ISS has been estimated with the change of total potential energy of the CNT-polymer system. The simulation results reveal that the vacancy defects significantly influence the ISS. Moreover, the simulation clarifies that CNT breakage occurs during the pull-out process for large size vacancy defect which ultimately reduces the reinforcement.