Silicon (Si)-based materials hold promise as the next-generation anodes for high-energy lithium (Li)-ion batteries. Enormous research efforts have been undertaken to mitigate the chemo-mechanical failure due to the large volume changes of Si during lithiation and delithiation cycles. It has been found that nanostructured Si coated with carbon or other functional materials can lead to significantly improved cyclability. However, the underlying mechanism and comparative performance of different coatings remain poorly understood. Herein, using in situ transmission electron microscopy (TEM) through a nanoscale half-cell battery, in combination with chemo-mechanical simulation, we explored the effect of thin (~5 nm) alucone and Al2O3 coatings on the lithiation kinetics of Si nanowires (SiNWs). We observed that the alucone coating leads to a "V-shaped" lithiation front of the SiNWs, while the Al2O3 coating yields an "H-shaped" lithiation front. These observations indicate that the difference between the Li surface diffusivity and bulk diffusivity of the coatings dictates lithiation induced morphological evolution in the nanowires. Our experiments also indicate that the reaction rate in the coating layer can be the limiting step for lithiation and therefore critically influences the rate performance of the battery. Further, the failure mechanism of the Al2O3 coated SiNWs was also explored. Our studies shed light on the design of high capacity, high rate and long cycle life Li-ion batteries.