Graphene is a novel two-dimensional material that could be used as an electrode material for lithium-ion batteries. However, the graphene folds and accumulates due to the interlayer van der Waals force, which severely affects the performance of graphene. In this work, mono-dispersed ZnO nanodots with the average size of 2.4 nm have been pinpointed on defects of graphene oxide by the homogeneous precipitation reaction between overdosed Zn2+ ions and N,N-Dimethylformamide. When used as the anode material of lithium-ion battery (LIBs), it shows good cycle stability and rate performance. After 350 cycles, the specific reversible capacity still reaches 978 mAh·g−1 , which is 76% of the initial reversible value. This work offers a general strategy to pinpoint well-distributed metal oxide nanodots on graphene defects.