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Background Low-temperature chilling is a major abiotic stress leading to reduced rice yield and is a significant environmental threat to food security. Low-temperature chilling studies have focused on physiological changes or coding genes. However, ceRNA mechanism in rice at low temperatures has not been reported. Therefore, to establish the ceRNA network and elucidate the transcriptional regulatory network and physiological mechanism of rice leaves in response to low-temperature stress, experiments were conducted using two rice (Oryza sativa. L) varieties with significantly different cold tolerances. Results The cold-tolerant variety has prolonged and relatively stable regulation of antioxidant enzymes (superoxide dismutase [SOD] and peroxidase [POD] catalase [CAT], and total antioxidant capacity) and osmotic substances (Proline [PRO], Soluble sugars [SS], and Soluble protein [SP]), which can remove harmful substances to maintain plant cell stability. Further screening based on VIP (variable importance in the projection) identified SOD and POD as two of the most essential antioxidant phenotypes. Furthermore, by combining antioxidant physiological indices with whole transcriptome data through weighted gene co-expression network analysis (WGCNA), the highly correlated modules were black and green, significantly associated with critical antioxidant indices (SOD and POD). Enrichment analysis revealed that black module genes were significantly enriched in the redox pathway. This module hub gene included UDP-glucosyltransferase family protein (Os05g0527000), sesquiterpene synthase (Os08g0167800), indole-3-glycerophosphatase gene (Os03g0797500), encoding oxidoreductase gene (Os04g0339400), and unknown genes (Os05g0212900). The green module genes were significantly enriched in the linoleic acid metabolic pathway. This module hub gene included WRKY transcription factor (Os11g0685700),abscisic acid (ABA) signal transduction pathway-related gene plasma membrane hydrogen-ATPase (Os02g0825600), Beta-Ig-containing H3 structural domain protein leucine-rich repeat-like receptor kinase (Os02g0615800), and two unknown genes (Os03g0103950 and Os08g0288050). Therefore, we selected module hub and significantly enriched pathway genes to construct key competing endogenous ceRNA networks. Both modules’ networks were integrated to obtain the ceRNA network of six lncRNAs regulating three co-expressed mRNAs through four miRNAs and six lncRNAs regulating two co-expressed mRNAs through four miRNAs. Finally, we performed preliminary gene sequence difference analysis, subcellular localization, and phenotypic validation of mutants for the putative glutamate protein OsGLR1.2 (Os02g0787600), which was previously thought to be associated with Ca2+ transport. Conclusions The results of this study reveal the characteristics of the response of rice to low temperature and provide insight into the mechanisms of regulation of rice to low temperature.