In rice (Oryza sativa L.), seeds exposed to heat stress during grain filling exhibit delayed germination because of DNA methylation levels at promoters of abscisic acid (ABA, a germination-inhibiting hormone) catabolism genes and α-amylase (starchhydrolyzing enzyme) genes, affecting their expression levels. Cold atmospheric plasma is known as an innovative and sustainable energy that has positive effects on the growth and development of many plant species. We, therefore, treated seeds that matured under heat stress with cold plasma and found that subsequent germination was significantly restored; genes involved in ABA biosynthesis (OsNCED2 and OsNCED5) were downregulated, whereas genes involved in ABA catabolism (OsABA8′OH1 and OsABA8′OH3) and α-amylase genes (OsAmy1A, OsAmy1C, OsAmy3B, and OsAmy3E) were upregulated. Cold plasma treatment caused significant hypermethylation of the OsNCED5 promoter and hypomethylation of OsAmy1C and OsAmy3E promoters, which matched their expression patterns. We suggest that cold plasma treatment can significantly improve the germination of rice seeds affected by heat stress by affecting epigenetic regulation.