Acute kidney injury related to cardiac surgery (CS-AKI) is a serious medical issue that creates significant social and economic challenges globally. Inflammatory responses and disruptions in water and salt balance are important contributors to CS-AKI. Earlier studies indicated that pre-surgery levels of NT-proBNP were a dependable indicator of CS-AKI. Emerging evidence indicates that the abnormal expression of microRNA (miRNA) and long non-coding RNA (lncRNA) plays a role in the occurrence of CS-AKI. However, the important roles and mechanisms by which NT-proBNP affects lncRNA and miRNA in CS-AKI are still unclear. Here, we investigated lncRNA and miRNA expression patterns in BNP-high, BNP-stable, AKI, and non-AKI groups through whole transcriptome sequencing analysis. The BNP group exhibited differential expressions of 105 miRNAs and 138 lncRNAs. We identified 7 common miRNAs and lncRNAs in both the BNP and AKI groups. A functional and pathway enrichment analysis of the target genes associated with these miRNAs and lncRNAs was conducted, indicating that miR-135a-5p, miR-138-5p, miR-143-3p, and miR-206 are key factors in CS-AKI, particularly in regulating inflammatory responses and water-salt balance. These results provide fresh perspectives on research directions and possible treatment approaches for CS-AKI.