Nano-drilling of multiwalled carbon nanotubes (MWCNTs) has been conducted by taking advantage of CoOx as the oxidation catalyst at a relatively low temperature of 250 °C. An increase of the ID/IG ratio of Raman spectroscopy, together with TEM visualization, justifies the presence of hole defects on the sidewalls, in comparison to the pristine and purified MWCNTs. Holes drilled on the basal plane of MWCNTs could increase access into the inner core as observed by the N2 adsorption isotherm. Drilled MWCNTs (DMWCNTs) show the largest quantity of functional groups of 5.4 × 10−3 mol g−1, which suggests that our drilling method also introduces functional groups on the edges. We also tested the electrochemical performance of our MWCNT samples as the anode material for lithium ion batteries. After 20 cycles at a current density of 25 mA h g−1, the specific discharge capacities of pristine, purified and DMWCNTs are 267, 421 and 625 mA h g−1, respectively. DMWCNTs exhibit the largest quantity of Li extraction from the GIC and inner core as shown by the dQ/dV discharge profiles. This suggests that increased access into the MWCNT inner core is proven to have positive effects on Li storage properties.