Li1.1V0.9O2/C microspheres with isomeric core‐shell structure were synthesized by a rapid cooling and subsequent evaporative assembly approach. The prepared Li1.1V0.9O2/C microspheres were characterized by X‐ray diffraction (XRD), Raman spectroscopy, scanning electron microscopy (SEM) including elemental mapping analysis, and transmission electron microscopy (TEM). The core‐shell Li1.1V0.9O2/C microspheres display identical composition but distinct texture of cores and shells, which herein is described as isomeric structure. Amorphous carbon nanodots are uniformly dispersed in the crystalline Li1.1V0.9O2 matrix in the core. In the shell however, Li1.1V0.9O2 nanoparticles are embedded in an amorphous carbon network. The Li1.1V0.9O2/C microspheres are tested as active material for anodes in lithium‐ion batteries, and exhibit an excellent reversible capacity of 295 mAh g−1, high capacity retention of 98 % after 100 cycles at 0.2 C and 95 % after 500 cycles at 2 C rate, and deliver wonderful rate capability of 250 mAh g−1 at 5 C. Thus, the Li1.1V0.9O2/C microspheres with isomeric core‐shell structure are promising candidates as anode material for commercial lithium‐ion batteries.