Solid-state cross-polarization magic-angle spinning carbon-13 nuclear magnetic resonance (13C CP/MAS NMR) spectroscopy is used to analyze starch derived from plants including wheat, maize, and potato, but few reports have described its application to rice starch. Here, we combined 13C CP/MAS NMR with deconvolution and subtraction methods to analyze rice lines including mutants that are deficient in at least one enzyme involved in amylose and/or amylopectin biosynthesis. We found that differences in the content of ordered structures between rice lines could be evaluated using C1 signal deconvolution and subtraction. The content of the V-type ordered structure increased with increasing amylose content. Furthermore, starch derived from a starch synthase (SS) IIIa/starch branching enzyme (BE) IIb-deficient mutant formed B- and V-type ordered structures and significantly more nonordered structures than the other rice lines. These data indicate that 13C CP/MAS NMR analysis is useful for discriminating the genetic backgrounds of starch derived from different rice cultivars.