Understanding the phase transition and Li-ion diffusion kinetics of Li-ion storage nanomaterials holds promising keys to further improve the cycle life and charge rate of the Li-ion battery. Traditional electrochemical studies were often based on a bulk electrode consisting of billions of electroactive nanoparticles, which washed out the intrinsic heterogeneity among individuals. Here, we employ optical microscopy, termed surface plasmon resonance microscopy (SPRM), to image electrochemical current of single LiCoO2 nanoparticles down to 50 fA during electrochemical cycling, from which the phase transition and Li-ion diffusion kinetics can be quantitatively resolved in a single nanoparticle, in operando and high throughput manner. SPRM maps the refractive index (RI) of single LiCoO2 nanoparticles, which significantly decreases with the gradual extraction of Li-ions, enabling the optical read-out of single nanoparticle electrochemistry. Further scanning electron microscopy characterization of the same batch of nanoparticles led to a bottom-up strategy for studying the structure-activity relationship. As RI is an intrinsic property of any material, the present approach is anticipated to be applicable for versatile kinds of anode and cathode materials, and to facilitate the rational design and optimization toward durable and fast-charging electrode materials.