Intervertebral disc degeneration (IDD) is the main cause of lower back pain. Lower back pain places a huge burden on society, and all current treatments for IDD cannot restore the original function of the intervertebral disc. Proposing new treatments for IDD requires clarifying the mechanisms of IDD. Physiological hypoxia is an important feature of the nucleus pulposus because of its special anatomical structure. Using RNA sequencing (RNA-seq), we obtained the whole transcriptome of nucleus pulposus cells (NPCs) under hypoxia and hypoxia-inducible factor (HIF1A) deletion. Results demonstrated possible effects of oxygen concentration and HIF1A on NPCs. In addition, our results showed that hypoxia can affect lipid metabolism in NPCs.