Nanoparticles having four different ratios of crystalline silicon (Si) cores and amorphous SiOx shells were synthesized by using a microwave-generated plasma. Their microstructures were analyzed to find quantitative relationships with electrochemical properties. By measuring XRD, SEM, HR-TEM, and Raman spectra of four samples with different core-shell microstructures, the quantitative fractions of crystalline Si core and amorphous SiOx shell in the nanoparticles were calculated. Also, electrochemical properties of the nanoparticles were measured and compared with the calculated fractions. The electrochemical properties such as the initial reversible capacity, the initial coulombic efficiency, and the capacity retention exhibited tendencies remarkably similar to those implied by the calculated fractions. Analysis of each sample's dQ/dV profile also gave us good evidence of understandable relationships between the fractions and electrochemical properties. Details of calculating the fractions from microstructural data are given, with suitable consideration having been given to the fact that several assumptions could lead to errors during the analysis. The approach introduced in this research offers a good means of analysis with which to further the optimal design of nanoparticle microstructure for Li-ion battery anodes.