Gastric cancer is a common heterogeneous malignancy that is pathologically characterized by the development of chronic atrophic gastritis and dysplasia of the epithelium. The pathogenic mechanisms at the molecular level are completely unclear. In the present study, we first address the expression network and miRNA–lncRNA–mRNA interaction in the malignant transformation process from normal mucosa and atrophic gastritis to a tumor. First, the long non-coding RNA (lncRNA), micro RNA (miRNA) and messenger RNA (mRNA) expression profiles of normal gastric mucosa, atrophic gastritis, gastric cancer and the peri-tumor tissues were analyzed using microarrays. Then, bioinformatic analyses were used to predict the gene targets and analyse their potential roles in tumorigenesis and progression of gastric cancer. Finally, an intersection analysis of microarray data showed that 10 miRNAs and 11 lncRNAs were detected in the malignant transformation process from normal mucosa tissues and atrophic gastritis to tumorigenesis, and many miRNAs and lncRNAs were novel and had important roles. Meanwhile, the significant pathways and biological functions regulated by the deregulated 21 non-coding genes were enriched. In conclusion, our work provides an important theoretical, experimental and clinical foundation for further research on more effective targets for the diagnosis, therapy and prognosis of gastric cancer.