Spinal cord injury (SCI) remains one of the most debilitating neurological disorders and the majority of SCI patients are in the chronic phase. Previous studies of SCI have usually focused on few genes and pathways at a time. In particular, the biological roles of long non-coding RNAs (lncRNAs) have never been characterized in SCI. Our study is the first to comprehensively investigate alterations in the expression of both coding and long non-coding genes in the sub-chronic and chronic stages of SCI using RNA-Sequencing. Through pathway analysis and network construction, the functions of differentially expressed genes were analyzed systematically. Furthermore, we predicted the potential regulatory function of non-coding transcripts, revealed enriched motifs of transcription factors in the upstream regulatory regions of differentially expressed lncRNAs, and identified differentially expressed lncRNAs homologous to human genomic regions which contain single-nucleotide polymorphisms associated with diseases. Overall, these results revealed critical pathways and networks that exhibit sustained alterations at the sub-chronic and chronic stages of SCI, highlighting the temporal regulation of pathological processes including astrogliosis. This study also provided an unprecedented resource and a new catalogue of lncRNAs potentially involved in the regulation and progression of SCI.