Objective Pathological alterations of the thymus are observed in the majority of patients with myasthenia gravis (MG). To explore the potential mechanisms of these alterations, we performed a transcriptome analysis and measured co-expression of aberrant long non-coding RNAs (lncRNAs) and messenger RNAs (mRNAs). Methods RNA was extracted from eight patients with thymoma, five of whom had MG. Transcriptome profiles were acquired through mRNA and lncRNA microarray analysis. Quantitative reverse transcription polymerase chain reaction was used to verify the results of the microarray analysis. LncRNAs co-expressed with mRNA were analyzed with Pearson's coefficient. Next, cis-regulated and trans-regulated target genes were predicted. The functions of aberrant lncRNAs were explored on the basis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of target mRNAs. Results The comparative microarray analysis identified 4360 lncRNAs and 2545 mRNAs with significant differential expression. The most significant GO enrichment terms were phosphoric ester hydrolase activity, phosphatase activity, and hydrolase activity, which were assigned as molecular functions. Regulation of endosome size was the most significant GO enrichment term assigned as a biological process, and Golgi apparatus was the most significant GO enrichment term assigned as cellular component. The reliability prediction terms of KEGG included calcium signaling pathway, glycosphingolipid biosynthesis, and caffeine metabolism. Conclusion MG-positive thymoma is associated with overactive biological processes and molecular functions, especially dephosphorylation and hydrolysis, which may affect thymocyte survival during selection in the thymus.