We synthesized silicon (Si) nanoparticles using an atmospheric microwave plasma process, and investigated the effects of hydrogen (H-2) injection on their microstructure during the synthesis. Two nozzles were applied to inject H-2 (swirling and rectilinear H-2). Our microstructural analysis indicated that the amount and method of H-2 injection were critical for completion of the reaction from silicon tetrachloride (SiCl4) to Si, as well as to obtain highly crystalline Si nanoparticles. The swirling H-2 was especially critical due to its formation of vortex flow, which allowed relatively long residence time of the H-ions in plasma. The Si nanoparticles synthesized by the atmospheric plasma process had core-shell structures that consisted of crystalline Si cores with amorphous SiOx shells of 5-15 nm thickness. We also investigated the feasibility of the synthesized Si nanoparticles as anode materials in a lithium-ion battery (LIB). For the core-shell structured Si nanoparticles, we obtained the first reversible capacity of 1204 mAhg(-1), and a capacity retention of 82.2% at the 50th cycle. (C) 2016 Elsevier B.V. All rights reserved.