The impact of CO2 sequestration on the host formation is an issue occurring over geologic time. Laboratory tests can provide important results to investigate this matter but have limitations due to a relatively short timeline. Based on literature review and core sample observation, naturally occurred geological phenomena, stylolites are studied in this paper for understanding CO2 sequestration in deep carbonate formations. Stylolites are distinctive and pervasive structures in carbonates that are related to water-assisted pressure solution. Pressure solution involving stylolitization is thought to be the main mechanism of compaction and cementation for many carbonates. In parallel, CO2 sequestration in carbonate formation involves extensive chemical reactions among water, CO2 and rock matrix, favoring chemical compaction as a consequence. An analogue between stylolites and CO2 sequestration induced formation heterogeneity exists in the sense of chemical compaction, as both pressure solution in stylolites and CO2 enriched solution in CO2 sequestration in carbonate formations may all introduce abnormal porous regions. The shear and/or tension fractures associated with stylolites zones may develop vertically or sub-vertically; all these give us alert for long-term safety of CO2 sequestration. Thus a study of stylolites will help to understand the CO2 sequestration in deep carbonate formation in the long run.