Objective To identify the potential pathological mechanisms of tuberculous spondylitis (TS). Methods Spinal specimens were collected from 13 TS patients and 13 controls who received treatment at a hospital from March 2021 to March 2023. Specimens were randomly selected from 3 TS patients and 3 controls to perform high-throughput lncRNAs and mRNAs sequencing with Illumina NovaSeq 6000. Differentially expressed lncRNAs (DELncRs) and mRNAs (DEmRs) in TS specimens were identified and analyzed through differential expression, and enrichment analysis was performed. The top 20 DEmRs with high connectivity were identified through protein-protein interaction (PPI) network. Regulatory network of DElncRs and DEmRs was built. Finally, gene expression of the remaining specimens was analyzed using qRT-PCR detection. Results A total of 1 243 DEmRs and 262 DElncRs were identified. Enrichment analysis revealed that muscle contraction, muscle system processes, muscle structural development, PI3K Akt signaling pathway, calcium signaling pathway, and cAMP signaling pathway were activated in TS, while responses to cytokines, cytokine-mediated signaling pathways, regulation of immune system processes, cytokine-cytokine receptor interactions, human T-cell leukemia virus type 1 infection, and phagosomes were inhibited in TS. Three sub-networks were identified in PPI, among which MYL1, TTN, LOC102723407, HLA-A, interleukin (IL)-6, and IL-1β had the highest connectivity and were identified as key DEmRs. MYL1, TTN, and IL-6 were regulated by DElncRs. qRT-PCR validated the differential expression of key DEmRs in TS. Conclusion DEmRs are regulated by lncRNAs and participate in the pathological process of TS, and the immune responses are inhibited in diseases condition. This study reveals key molecules and signaling pathways in TS, providing new insights into the pathological mechanisms of TS, and suggest scientific basis for developing new therapeutic targets.