The effect of mechanical milling on the formation of short titanate nanotube and structural change induced is investigated. Mechanical milling produces the short nanotubes with the length of 30–160 nm. The lithium ion intercalation characteristics of the obtained short titanate nanotube were studied to verify the effect of the newly formed cross-sections of nanotubes. It was found that the protonated titanate nanotubes maintained long shapes until 30 min of mechanical milling and were transformed into agglomerated nanosheets and finally anatase granules depending on the treatment duration. Through galvanostatic investigation, the nanotubes with milling of 15 min exhibited the highest discharge capacity of 336 mAh·g −1in first cycle, 12.4% larger than pristine.