Many lncRNAs have been shown to play a vital role in aging processes. However, how lncRNAs regulate seed aging remains unknown. In this study, we performed whole transcriptome strand-specific RNA sequencing of samples from rice embryos, analyzed the differences in expression of rice seed lncRNAs before and after artificial aging treatment (AAT), and systematically screened 6002 rice lncRNAs. During the AAT period, the expression levels of most lncRNAs (454) were downregulated and only four were upregulated among the 458 differentially expressed lncRNAs (DELs). Cis- or trans-regulated target genes of the four upregulated lncRNAs were mainly related to base repair, while 454 downregulated lncRNAs were related to plant–pathogen interaction, plant hormones, energy metabolism, and secondary metabolism. The pathways of DEL target genes were similar with those of differentially expressed mRNAs (DEGs). A competing endogenous RNA (ceRNA) network composed of 34 lncRNAs, 24 microRNAs (miRNA), and 161 mRNAs was obtained. The cDNA sequence of lncRNA LNC_037529 was obtained by rapid amplification of cDNA ends (RACE) cloning with a total length of 1325 bp, a conserved 5′ end, and a non-conserved 3′ end. Together, our findings indicate that genome-wide selection for lncRNA downregulation was an important mechanism for rice seed aging. LncRNAs can be used as markers of seed aging in rice. These findings provide a future path to decipher the underlying mechanism associated with lncRNAs in seed aging.