In this paper, 3D hollow framework of GeOx is synthesized using a bubble-template hydrothermal procedure. The as-obtained hollow structure exhibits excellent cycling performance and rate capability in comparison with GeOx nanoparticles when used as an anode material in lithium ion batteries. The GeOx 3D hollow framework shows a high capacity of up to 1480 mAh·g−1 and 1109 mAh·g−1 at 80 mA·g−1 and 1600 mA·g−1 current density, respectively. The excellent lithium storage performance can be attributed to the unique 3D hollow framework. The framework not only acts as the buffer layer to alleviate the strain during lithiation, but also facilitates the electron transfer during the charge/discharge processes.