Intervertebral disc degeneration (IDD) represents one of the leading causes of low back pain. Research suggests the participation of LINC01116 in IDD progression. Herein, the current study explored the underlying mechanism of LINC01116 in IDD. The differential expression patterns of LINC01116 in IDD and normal tissues were analyzed using the GEO database. Human nucleus pulposus (NP) cells were provided and treated with IL-1β to establish IDD models in vitro. LINC01116 expression was detected and intervened. Indices such as cell proliferation, apoptosis, and extracellular matrix (ECM)-related factor expression were determined using CCK-8 assay, flow cytometry, and Western blotting. LINC01116 sublocation was identified by means of nuclear/cytosol fractionation assay. The binding relationships between LINC01116 and miR-9-5p and miR-9-5p and ZIC5 were verified by bioinformatics analysis, dual-luciferase assays, RNA immunoprecipitation (RIP) assay, and RNA-pull-down. Western blotting was conducted to measure the levels of the Wnt pathway key factors. LINC01116 was highly expressed in the degenerative NP cells. Silencing of LINC01116 critically promoted degenerative NP cell proliferation and inhibited apoptosis and ECM loss. LINC01116 was located in the cytoplasm. In degenerative NP cell models, LINC01116 could competitively bind to miR-9-5p to elevate ZIC5 expression. LINC01116 induced NP cell apoptosis and impeded NP cell proliferation and ECM synthesis by inhibiting miR-9-5p and miR-9-5p targeted ZIC5. ZIC5 could effectively increase the levels of the Wnt pathway-related factors. Silencing LINC01116 blocked its adsorption of miR-9-5p as a sponge to promote the miR-9- 5p expression and inhibit ZIC5/Wnt activation, thus impacting NP cell biological functions.