Recently, metal phosphides have been investigated as potential anode materials because of higher specific capacity compared with those of carbonaceous materials. However, the rapid capacity fade upon cycling leads to poor durability and short cycle life, which cannot meet the need of lithium-ion batteries with high energy density. Herein, we report a layer-structured GeP3/C nanocomposite anode material with high performance prepared by a facial and large-scale ball milling method via in-situ mechanical reaction. The P-O-C bonds are formed in the composite, leading to close contact between GeP3 and carbon. As a result, the GeP3/C anode displays excellent lithium storage performance with a high reversible capacity up to 1109 mA h g−1 after 130 cycles at a current density of 0.1 A g−1. Even at high current densities of 2 and 5 A g−1, the reversible capacities are still as high as 590 and 425 mA h g−1, respectively. This suggests that the GeP3/C composite is promising to achieve high-energy lithium-ion batteries and the mechanical milling is an efficient method to fabricate such composite electrode materials especially for large-scale application.