Knockout of FOXO3was found to impair IVD maturation and homeostasis in postnatal mice as well as facilitating extracellular matrix (ECM) degradation. RNA sequencing can uncover disease-related gene expression and investigate disease pathophysiology. High-throughput transcriptome sequencing and experimental validations were used to identify the essential gene and mechanism involved in intervertebral disc degeneration (IDD). Nucleus pulposus (NP) tissue samples were collected from the mice with conditional knockout of FOXO3(FOXO3KO) for high-throughput sequencing, followed by screening of differentially expressed lncRNAs and mRNAs. The mRNAs were subjected to GO and KEGG enrichment analyses. Interactions among FOXO3, HOTTIP, miR-615-3pand COL2A1were analyzed. NP cells were subjected to a series of mimics, inhibitors, overexpression plasmids and shRNAs to validate the mechanisms of FOXO3in controlling of HOTTIP/miR-615-3p/COL2A1in IDD. Mechanistically, FOXO3transcriptionally activated HOTTIP, facilitated the competitive HOTTIPbinding to miR-615-3pand increased the expression of the miR-615-3ptarget gene COL2A1. Thus, NP cell proliferation was induced, cell apoptosis was diminished, resulting in delayed development of IDD. Conclusively, the transcription factor FOXO3may decrease miR-615-3pbinding to COL2A1and upregulate COL2A1expression by activating HOTTIPtranscription, which in turn inhibits NP cell apoptosis and promotes its proliferation, to prevent the degradation of intervertebral disc matrix, maintain the normal physiological function of intervertebral disc, thereby preventing the occurrence and development of IVDD.