Background: The pathological development of colon cancer is a complex progression that depends on multiple alterations of coding and non-coding genes. Colon cancer are challenged by the immune system and acquire features to evade its surveillance during the whole process of occurrence and development. Therefore, it is important to capture the immune regulatory events during the progression of colon cancer development and to identify reliable markers for predicting clinical outcomes in patients. Methods: Here, a standardized computational procedures was developed to evaluate immune cell populations-associated gene (immuneCPa gene)-lncRNA relationships in diverse stages (I, II, III and IV) of colon cancer based on genes and lncRNAs expression. Stage-specific immuneCPa genes and lncRNAs were identified in each colon cancer stage. Results: Dynamic stage-specific immuneCPa gene-lncRNA regulatory networks were constructed and characterized in colon cancer development. A immuneCPa gene-lncRNA activity profile across different stages revealed that lncRNAs were highly stage-selective in regulating immuneCPa genes in colon cancer. Specify scores of immune indicated that diverse kinds of immune cells were temporally-specific in colon cancer. NK CD56bright cell showed strongest stage common features in colon cancer. Further survival analysis indicated that some stage specific immuneCPa gene-lncRNA relationships may have the potential for predicting colon cancer prognosis. Conclusions: Collectively, our study leads to a novel starting point for future functional explorations, the identification of immune-related biomarkers, and lncRNA-based targeted therapy for colon cancer.